1
|
Esposito M, Minnai F, Copetti M, Miscio G, Perna R, Piepoli A, De Vincentis G, Benvenuto M, D'Addetta P, Croci S, Baldassarri M, Bruttini M, Fallerini C, Brugnoni R, Cavalcante P, Baggi F, Corsini EMG, Ciusani E, Andreetta F, Dragani TA, Fratelli M, Carella M, Mantegazza RE, Renieri A, Colombo F. Human leukocyte antigen variants associate with BNT162b2 mRNA vaccine response. Commun Med (Lond) 2024; 4:63. [PMID: 38575714 PMCID: PMC10995155 DOI: 10.1038/s43856-024-00490-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 03/21/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Since the beginning of the anti-COVID-19 vaccination campaign, it has become evident that vaccinated subjects exhibit considerable inter-individual variability in the response to the vaccine that could be partly explained by host genetic factors. A recent study reported that the immune response elicited by the Oxford-AstraZeneca vaccine in individuals from the United Kingdom was influenced by a specific allele of the human leukocyte antigen gene HLA-DQB1. METHODS We carried out a genome-wide association study to investigate the genetic determinants of the antibody response to the Pfizer-BioNTech vaccine in an Italian cohort of 1351 subjects recruited in three centers. Linear regressions between normalized antibody levels and genotypes of more than 7 million variants was performed, using sex, age, centers, days between vaccination boost and serological test, and five principal components as covariates. We also analyzed the association between normalized antibody levels and 204 HLA alleles, with the same covariates as above. RESULTS Our study confirms the involvement of the HLA locus and shows significant associations with variants in HLA-A, HLA-DQA1, and HLA-DQB1 genes. In particular, the HLA-A*03:01 allele is the most significantly associated with serum levels of anti-SARS-CoV-2 antibodies. Other alleles, from both major histocompatibility complex class I and II are significantly associated with antibody levels. CONCLUSIONS These results support the hypothesis that HLA genes modulate the response to Pfizer-BioNTech vaccine and highlight the need for genetic studies in diverse populations and for functional studies aimed to elucidate the relationship between HLA-A*03:01 and CD8+ cell response upon Pfizer-BioNTech vaccination.
Collapse
Affiliation(s)
- Martina Esposito
- National Research Council, Institute for Biomedical Technologies, Segrate, MI, Italy
| | - Francesca Minnai
- National Research Council, Institute for Biomedical Technologies, Segrate, MI, Italy
- Department of Medical Biotechnology and Translational Medicine (BioMeTra), Università degli Studi di Milano, Milan, Italy
| | - Massimiliano Copetti
- Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Giuseppe Miscio
- Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Rita Perna
- Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Ada Piepoli
- Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | | | - Mario Benvenuto
- Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Paola D'Addetta
- Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Susanna Croci
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | - Margherita Baldassarri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | - Mirella Bruttini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Chiara Fallerini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | | | | | - Fulvio Baggi
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | | | - Emilio Ciusani
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | | | | | | | - Massimo Carella
- Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | | | - Alessandra Renieri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Francesca Colombo
- National Research Council, Institute for Biomedical Technologies, Segrate, MI, Italy.
| |
Collapse
|
2
|
David R, Rybina A, Burel J, Heriche J, Audergon P, Boiten J, Coppens F, Crockett S, Exter K, Fahrner S, Fratelli M, Goble C, Gormanns P, Grantner T, Grüning B, Gurwitz KT, Hancock JM, Harmse H, Holub P, Juty N, Karnbach G, Karoune E, Keppler A, Klemeier J, Lancelotti C, Legras J, Lister AL, Longo DL, Ludwig R, Madon B, Massimi M, Matser V, Matteoni R, Mayrhofer MT, Ohmann C, Panagiotopoulou M, Parkinson H, Perseil I, Pfander C, Pieruschka R, Raess M, Rauber A, Richard AS, Romano P, Rosato A, Sánchez‐Pla A, Sansone S, Sarkans U, Serrano‐Solano B, Tang J, Tanoli Z, Tedds J, Wagener H, Weise M, Westerhoff HV, Wittner R, Ewbank J, Blomberg N, Gribbon P. "Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling. EMBO J 2023; 42:e115008. [PMID: 37964598 PMCID: PMC10690449 DOI: 10.15252/embj.2023115008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/12/2023] [Accepted: 09/18/2023] [Indexed: 11/16/2023] Open
Abstract
The main goals and challenges for the life science communities in the Open Science framework are to increase reuse and sustainability of data resources, software tools, and workflows, especially in large-scale data-driven research and computational analyses. Here, we present key findings, procedures, effective measures and recommendations for generating and establishing sustainable life science resources based on the collaborative, cross-disciplinary work done within the EOSC-Life (European Open Science Cloud for Life Sciences) consortium. Bringing together 13 European life science research infrastructures, it has laid the foundation for an open, digital space to support biological and medical research. Using lessons learned from 27 selected projects, we describe the organisational, technical, financial and legal/ethical challenges that represent the main barriers to sustainability in the life sciences. We show how EOSC-Life provides a model for sustainable data management according to FAIR (findability, accessibility, interoperability, and reusability) principles, including solutions for sensitive- and industry-related resources, by means of cross-disciplinary training and best practices sharing. Finally, we illustrate how data harmonisation and collaborative work facilitate interoperability of tools, data, solutions and lead to a better understanding of concepts, semantics and functionalities in the life sciences.
Collapse
|
3
|
Fosse V, Oldoni E, Bietrix F, Budillon A, Daskalopoulos EP, Fratelli M, Gerlach B, Groenen PMA, Hölter SM, Menon JML, Mobasheri A, Osborne N, Ritskes-Hoitinga M, Ryll B, Schmitt E, Ussi A, Andreu AL, McCormack E, Demotes J, Garcia P, Gerardi C, Glaab E, Haro JM, Hulstaert F, Miguel LS, Mirete JS, Niubo AS, Porcher R, Rauschenberger A, Rodriguez MC, Superchi C, Torres T. Recommendations for robust and reproducible preclinical research in personalised medicine. BMC Med 2023; 21:14. [PMID: 36617553 PMCID: PMC9826728 DOI: 10.1186/s12916-022-02719-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Personalised medicine is a medical model that aims to provide tailor-made prevention and treatment strategies for defined groups of individuals. The concept brings new challenges to the translational step, both in clinical relevance and validity of models. We have developed a set of recommendations aimed at improving the robustness of preclinical methods in translational research for personalised medicine. METHODS These recommendations have been developed following four main steps: (1) a scoping review of the literature with a gap analysis, (2) working sessions with a wide range of experts in the field, (3) a consensus workshop, and (4) preparation of the final set of recommendations. RESULTS Despite the progress in developing innovative and complex preclinical model systems, to date there are fundamental deficits in translational methods that prevent the further development of personalised medicine. The literature review highlighted five main gaps, relating to the relevance of experimental models, quality assessment practices, reporting, regulation, and a gap between preclinical and clinical research. We identified five points of focus for the recommendations, based on the consensus reached during the consultation meetings: (1) clinically relevant translational research, (2) robust model development, (3) transparency and education, (4) revised regulation, and (5) interaction with clinical research and patient engagement. Here, we present a set of 15 recommendations aimed at improving the robustness of preclinical methods in translational research for personalised medicine. CONCLUSIONS Appropriate preclinical models should be an integral contributor to interventional clinical trial success rates, and predictive translational models are a fundamental requirement to realise the dream of personalised medicine. The implementation of these guidelines is ambitious, and it is only through the active involvement of all relevant stakeholders in this field that we will be able to make an impact and effectuate a change which will facilitate improved translation of personalised medicine in the future.
Collapse
Affiliation(s)
- Vibeke Fosse
- Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, Bergen, Norway.
| | - Emanuela Oldoni
- EATRIS ERIC, European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
| | - Florence Bietrix
- EATRIS ERIC, European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
| | - Alfredo Budillon
- Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione G. Pascale" - IRCCS, Naples, Italy
| | | | - Maddalena Fratelli
- Department of Biochemistry and Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Björn Gerlach
- PAASP GmbH, Guarantors of EQIPD e.V., Central Institute for Mental Health in Mannheim, Mannheim, Germany
| | | | | | - Julia M L Menon
- Preclinicaltrials.eu, Netherlands Heart Institute, Utrecht, The Netherlands
| | - Ali Mobasheri
- Research Unit of Medical Imaging, Physics and Technology, Faculty of Medicine, University of Oulu, 90570, Oulu, Finland.,Department of Regenerative Medicine, State Research Institute Centre for Innovative Medicine, LT-08406, Vilnius, Lithuania.,Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China.,Departments of Orthopedics, Rheumatology and Clinical Immunology, University Medical Center Utrecht, 508, GA, Utrecht, The Netherlands.,World Health Organization Collaborating Centre for Public Health Aspects of Musculoskeletal Health and Aging, Université de Liège, B-4000, Liège, Belgium
| | | | - Merel Ritskes-Hoitinga
- Department of Population Health Sciences, IRAS, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Department of Clinical Medicine, AUGUST, Aarhus University, Aarhus, Denmark
| | - Bettina Ryll
- Melanoma Patient Network Europe, Uppsala, Sweden
| | - Elmar Schmitt
- Global Regulatory Oncology, Merck Healthcare KGaA, Frankfurter Str. 250, 64293, Darmstadt, Germany
| | - Anton Ussi
- EATRIS ERIC, European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
| | - Antonio L Andreu
- EATRIS ERIC, European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
| | - Emmet McCormack
- Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, Bergen, Norway.,Department of Clinical Science, Centre for Pharmacy, The University of Bergen, Bergen, Norway
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Gianni M, Terao M, Kurosaki M, Paroni G, Brunelli L, Pastorelli R, Zanetti A, Lupi M, Acquavita A, Bolis M, Fratelli M, Rochette-Egly C, Garattini E. Correction: S100A3 a partner protein regulating the stability/activity of RARα and PML-RARα in cellular models of breast/lung cancer and acute myeloid leukemia. Oncogene 2023; 42:254-258. [PMID: 36476834 PMCID: PMC9836929 DOI: 10.1038/s41388-022-02564-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Maurizio Gianni
- grid.4527.40000000106678902Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156 Milano, Italy
| | - Mineko Terao
- grid.4527.40000000106678902Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156 Milano, Italy
| | - Mami Kurosaki
- grid.4527.40000000106678902Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156 Milano, Italy
| | - Gabriela Paroni
- grid.4527.40000000106678902Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156 Milano, Italy
| | - Laura Brunelli
- grid.4527.40000000106678902Laboratory of Mass Spectrometry, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156 Milano, Italy
| | - Roberta Pastorelli
- grid.4527.40000000106678902Laboratory of Mass Spectrometry, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156 Milano, Italy
| | - Adriana Zanetti
- grid.4527.40000000106678902Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156 Milano, Italy
| | - Monica Lupi
- grid.4527.40000000106678902Laboratory of Cancer Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156 Milano, Italy
| | - Andrea Acquavita
- grid.4527.40000000106678902Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156 Milano, Italy
| | - Marco Bolis
- grid.4527.40000000106678902Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156 Milano, Italy
| | - Maddalena Fratelli
- grid.4527.40000000106678902Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156 Milano, Italy
| | - Cecile Rochette-Egly
- grid.11843.3f0000 0001 2157 9291Department of Functional Genomics and Cancer, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM, U964; CNRS, UMR7104, Université de Strasbourg, 1 rue Laurent Fries, BP 10142, 67404 Illkirch Cedex, France
| | - Enrico Garattini
- grid.4527.40000000106678902Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156 Milano, Italy
| |
Collapse
|
5
|
Mendogni P, Affatato R, Cabri E, Chiappa M, Ndembe G, Tosi D, Del Gobbo A, Fratelli M, Pardini E, Petrini I, Rosso L, Broggini M, Marabese M. Isolation and characterization of two newly established thymoma PDXs from two relapses of the same patient: a new tool to investigate thymic malignancies. J Exp Clin Cancer Res 2022; 41:343. [PMID: 36517829 PMCID: PMC9749328 DOI: 10.1186/s13046-022-02554-4] [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] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Thymic malignancies are a heterogeneous group of rare cancers for which systemic chemotherapy is the standard treatment in the setting of advanced, recurrent or refractory diseases. Both environmental and genetic risk factors have not been fully clarified and few target-specific drugs have been developed for thymic epithelial tumors. A major challenge in studying thymic epithelial tumors is the lack of preclinical models for translational studies. MAIN BODY Starting from bioptic material of two consecutive recurrences of the same patient, we generated two patient-derived xenografts. The patient-derived xenografts models were characterized for histology by immunohistochemistry and mutations using next-generation sequencing. When compared to the original tumors resected from the patient, the two patient-derived xenografts had preserved morphology after the stain with hematoxylin and eosin, although there was a moderate degree of de-differentiation. From a molecular point of view, the two patient-derived xenografts maintained 74.3 and 61.8% of the mutations present in the human tumor of origin. SHORT CONCLUSION The newly generated patient-derived xenografts recapitulate both the molecular characteristics and the evolution of the thymoma it derives from well, allowing to address open questions for this rare cancer.
Collapse
Affiliation(s)
- Paolo Mendogni
- grid.414818.00000 0004 1757 8749Thoracic Surgery and Lung Transplant Unit, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Roberta Affatato
- grid.4527.40000000106678902Laboratory of Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Enrico Cabri
- grid.4527.40000000106678902Department of Biochemistry, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Michela Chiappa
- grid.4527.40000000106678902Laboratory of Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Gloriana Ndembe
- grid.4527.40000000106678902Laboratory of Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Davide Tosi
- grid.414818.00000 0004 1757 8749Thoracic Surgery and Lung Transplant Unit, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Alessandro Del Gobbo
- grid.414818.00000 0004 1757 8749Division of Pathology, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Maddalena Fratelli
- grid.4527.40000000106678902Department of Biochemistry, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Eleonora Pardini
- grid.144189.10000 0004 1756 8209Department of Translational Research & New Technologies in Surgery and Medicine, University of Pisa and Azienda Ospedaliero Universitaria Pisana, 56100 Pisa, Italy
| | - Iacopo Petrini
- grid.144189.10000 0004 1756 8209Department of Translational Research & New Technologies in Surgery and Medicine, University of Pisa and Azienda Ospedaliero Universitaria Pisana, 56100 Pisa, Italy
| | - Lorenzo Rosso
- grid.414818.00000 0004 1757 8749Thoracic Surgery and Lung Transplant Unit, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Massimo Broggini
- grid.4527.40000000106678902Laboratory of Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Mirko Marabese
- grid.4527.40000000106678902Laboratory of Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| |
Collapse
|
6
|
Fosse V, Oldoni E, Gerardi C, Banzi R, Fratelli M, Bietrix F, Ussi A, Andreu AL, McCormack E. Evaluating Translational Methods for Personalized Medicine—A Scoping Review. J Pers Med 2022; 12:jpm12071177. [PMID: 35887673 PMCID: PMC9324577 DOI: 10.3390/jpm12071177] [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: 05/24/2022] [Revised: 07/10/2022] [Accepted: 07/16/2022] [Indexed: 12/09/2022] Open
Abstract
The introduction of personalized medicine, through the increasing multi-omics characterization of disease, brings new challenges to disease modeling. The scope of this review was a broad evaluation of the relevance, validity, and predictive value of the current preclinical methodologies applied in stratified medicine approaches. Two case models were chosen: oncology and brain disorders. We conducted a scoping review, following the Joanna Briggs Institute guidelines, and searched PubMed, EMBASE, and relevant databases for reports describing preclinical models applied in personalized medicine approaches. A total of 1292 and 1516 records were identified from the oncology and brain disorders search, respectively. Quantitative and qualitative synthesis was performed on a final total of 63 oncology and 94 brain disorder studies. The complexity of personalized approaches highlights the need for more sophisticated biological systems to assess the integrated mechanisms of response. Despite the progress in developing innovative and complex preclinical model systems, the currently available methods need to be further developed and validated before their potential in personalized medicine endeavors can be realized. More importantly, we identified underlying gaps in preclinical research relating to the relevance of experimental models, quality assessment practices, reporting, regulation, and a gap between preclinical and clinical research. To achieve a broad implementation of predictive translational models in personalized medicine, these fundamental deficits must be addressed.
Collapse
Affiliation(s)
- Vibeke Fosse
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway;
- Correspondence:
| | - Emanuela Oldoni
- EATRIS ERIC, European Infrastructure for Translational Medicine, 1081 HZ Amsterdam, The Netherlands; (E.O.); (F.B.); (A.U.); (A.L.A.)
| | - Chiara Gerardi
- Centre for Health Regulatory Policies, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (C.G.); (R.B.)
| | - Rita Banzi
- Centre for Health Regulatory Policies, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy; (C.G.); (R.B.)
| | - Maddalena Fratelli
- Department of Biochemistry and Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy;
| | - Florence Bietrix
- EATRIS ERIC, European Infrastructure for Translational Medicine, 1081 HZ Amsterdam, The Netherlands; (E.O.); (F.B.); (A.U.); (A.L.A.)
| | - Anton Ussi
- EATRIS ERIC, European Infrastructure for Translational Medicine, 1081 HZ Amsterdam, The Netherlands; (E.O.); (F.B.); (A.U.); (A.L.A.)
| | - Antonio L. Andreu
- EATRIS ERIC, European Infrastructure for Translational Medicine, 1081 HZ Amsterdam, The Netherlands; (E.O.); (F.B.); (A.U.); (A.L.A.)
| | - Emmet McCormack
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, 5021 Bergen, Norway;
- Centre for Pharmacy, Department of Clinical Science, The University of Bergen, 5021 Bergen, Norway
| | | |
Collapse
|
7
|
Chilà R, Chiappa M, Guffanti F, Panini N, Conconi D, Rinaldi A, Cascione L, Bertoni F, Fratelli M, Damia G. Stable CDK12 Knock-Out Ovarian Cancer Cells Do Not Show Increased Sensitivity to Cisplatin and PARP Inhibitor Treatment. Front Oncol 2022; 12:903536. [PMID: 35912188 PMCID: PMC9328802 DOI: 10.3389/fonc.2022.903536] [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: 03/25/2022] [Accepted: 05/24/2022] [Indexed: 11/23/2022] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) is a serine/threonine kinase involved in the regulation of RNA polymerase II and in the transcription of a subset of genes involved in the DNA damage response. CDK12 is one of the most mutated genes in ovarian carcinoma. These mutations result in loss-of-function and can predict the responses to PARP1/2 inhibitor and platinum. To investigate the role of CDK12 in ovarian cancer, CRISPR/Cas9 technology was used to generate a stable CDK12 knockout (KO) clone in A2780 ovarian carcinoma cells. This is the first report on a CDK12 null cell line. The clone had slower cell growth and was less clonogenic than parental cells. These data were confirmed in vivo, where CDK12 KO transplanted cells had a much longer time lag and slightly slower growth rate than CDK12-expressing cells. The slower growth was associated with a higher basal level of apoptosis, but there were no differences in the basal level of autophagy and senescence. While cell cycle distribution was similar in parental and knockout cells, there was a doubling in DNA content, with an almost double modal number of chromosomes in the CDK12 KO clone which, however did not display any increase in γH2AX, a marker of DNA damage. We found partial down-regulation of the expression of DNA repair genes at the mRNA level and, among the down-regulated genes, an enrichment in the G2/M checkpoint genes. Although the biological features of CDK12 KO cells are compatible with the function of CDK12, contrary to some reports, we could not find any difference in the sensitivity to cisplatin and olaparib between wild-type and CDK12 KO cells.
Collapse
Affiliation(s)
- Rosaria Chilà
- Laboratory of Experimental Oncology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri Istituito di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Michela Chiappa
- Laboratory of Experimental Oncology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri Istituito di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Federica Guffanti
- Laboratory of Experimental Oncology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri Istituito di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Nicolò Panini
- Laboratory of Cancer Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Donatella Conconi
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Andrea Rinaldi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland
| | - Maddalena Fratelli
- Department of Biochemistry, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Giovanna Damia
- Laboratory of Experimental Oncology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri Istituito di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
- *Correspondence: Giovanna Damia,
| |
Collapse
|
8
|
Fallerini C, Picchiotti N, Baldassarri M, Zguro K, Daga S, Fava F, Benetti E, Amitrano S, Bruttini M, Palmieri M, Croci S, Lista M, Beligni G, Valentino F, Meloni I, Tanfoni M, Minnai F, Colombo F, Cabri E, Fratelli M, Gabbi C, Mantovani S, Frullanti E, Gori M, Crawley FP, Butler-Laporte G, Richards B, Zeberg H, Lipcsey M, Hultström M, Ludwig KU, Schulte EC, Pairo-Castineira E, Baillie JK, Schmidt A, Frithiof R, Mari F, Renieri A, Furini S. Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity. Hum Genet 2022; 141:147-173. [PMID: 34889978 PMCID: PMC8661833 DOI: 10.1007/s00439-021-02397-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 09/14/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022]
Abstract
The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management.
Collapse
Affiliation(s)
- Chiara Fallerini
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Nicola Picchiotti
- grid.9024.f0000 0004 1757 4641University of Siena, DIISM-SAILAB, Siena, Italy ,grid.8982.b0000 0004 1762 5736Department of Mathematics, University of Pavia, Pavia, Italy
| | - Margherita Baldassarri
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Kristina Zguro
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
| | - Sergio Daga
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Francesca Fava
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy ,grid.411477.00000 0004 1759 0844Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Elisa Benetti
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
| | - Sara Amitrano
- grid.411477.00000 0004 1759 0844Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Mirella Bruttini
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy ,grid.411477.00000 0004 1759 0844Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Maria Palmieri
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Susanna Croci
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Mirjam Lista
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Giada Beligni
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Floriana Valentino
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Ilaria Meloni
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Marco Tanfoni
- grid.9024.f0000 0004 1757 4641University of Siena, DIISM-SAILAB, Siena, Italy
| | - Francesca Minnai
- grid.429135.80000 0004 1756 2536Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche, Segrate, MI Italy
| | - Francesca Colombo
- grid.429135.80000 0004 1756 2536Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche, Segrate, MI Italy
| | - Enrico Cabri
- grid.4527.40000000106678902Pharmacogenomics Unit, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Maddalena Fratelli
- grid.4527.40000000106678902Pharmacogenomics Unit, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Chiara Gabbi
- grid.4714.60000 0004 1937 0626Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Stefania Mantovani
- grid.419425.f0000 0004 1760 3027Department of Medicine, Clinical Immunology and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Elisa Frullanti
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Marco Gori
- grid.9024.f0000 0004 1757 4641University of Siena, DIISM-SAILAB, Siena, Italy ,grid.503321.60000 0001 0561 3840Models and Algorithms for Artificial Intelligence (MAASAI) Research Group, Université Côte d’Azur, Inria, CNRS, I3S, Biot, France
| | - Francis P. Crawley
- Good Clinical Practice Alliance-Europe (GCPA) and Strategic Initiative for Developing Capacity in Ethical Review (SIDCER), Leuven, Belgium
| | - Guillaume Butler-Laporte
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC Canada ,grid.14709.3b0000 0004 1936 8649Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC Canada
| | - Brent Richards
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC Canada ,grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montreal, QC Canada ,grid.13097.3c0000 0001 2322 6764Department of Twin Research, King’s College London, London, UK
| | - Hugo Zeberg
- grid.4714.60000 0004 1937 0626Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Miklos Lipcsey
- grid.8993.b0000 0004 1936 9457Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden ,grid.8993.b0000 0004 1936 9457Hedenstierna Laboratory, CIRRUS, Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Michael Hultström
- grid.8993.b0000 0004 1936 9457Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden ,grid.8993.b0000 0004 1936 9457Integrative Physiology, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Kerstin U. Ludwig
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Eva C. Schulte
- grid.411095.80000 0004 0477 2585Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, 80336 Munich, Germany ,grid.5252.00000 0004 1936 973XDepartment of Psychiatry and Psychotherapy, University Hospital, LMU Munich, 80336 Munich, Germany ,grid.6936.a0000000123222966Institute of Virology, Technical University Munich/Helmholtz Zentrum München, Munich, Germany
| | - Erola Pairo-Castineira
- grid.4305.20000 0004 1936 7988MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU UK ,grid.4305.20000 0004 1936 7988Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG UK
| | - John Kenneth Baillie
- grid.4305.20000 0004 1936 7988MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU UK ,grid.4305.20000 0004 1936 7988Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG UK ,grid.418716.d0000 0001 0709 1919Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, H16 5SA UK
| | - Axel Schmidt
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Robert Frithiof
- grid.8993.b0000 0004 1936 9457Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | | | | | | | - Francesca Mari
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy ,grid.411477.00000 0004 1759 0844Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Alessandra Renieri
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy. .,Medical Genetics, University of Siena, Siena, Italy. .,Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy. .,Medical Genetics Unit, University of Siena, Policlinico Le Scotte, Viale Bracci, 2, 53100, Siena, Italy.
| | - Simone Furini
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
| |
Collapse
|
9
|
Regondi C, Fratelli M, Damia G, Guffanti F, Ganzinelli M, Matteucci M, Masseroli M. Predictive modeling of gene expression regulation. BMC Bioinformatics 2021; 22:571. [PMID: 34837938 PMCID: PMC8626902 DOI: 10.1186/s12859-021-04481-1] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 11/15/2021] [Indexed: 11/24/2022] Open
Abstract
Background In-depth analysis of regulation networks of genes aberrantly expressed in cancer is essential for better understanding tumors and identifying key genes that could be therapeutically targeted. Results We developed a quantitative analysis approach to investigate the main biological relationships among different regulatory elements and target genes; we applied it to Ovarian Serous Cystadenocarcinoma and 177 target genes belonging to three main pathways (DNA REPAIR, STEM CELLS and GLUCOSE METABOLISM) relevant for this tumor. Combining data from ENCODE and TCGA datasets, we built a predictive linear model for the regulation of each target gene, assessing the relationships between its expression, promoter methylation, expression of genes in the same or in the other pathways and of putative transcription factors. We proved the reliability and significance of our approach in a similar tumor type (basal-like Breast cancer) and using a different existing algorithm (ARACNe), and we obtained experimental confirmations on potentially interesting results. Conclusions The analysis of the proposed models allowed disclosing the relations between a gene and its related biological processes, the interconnections between the different gene sets, and the evaluation of the relevant regulatory elements at single gene level. This led to the identification of already known regulators and/or gene correlations and to unveil a set of still unknown and potentially interesting biological relationships for their pharmacological and clinical use. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04481-1.
Collapse
Affiliation(s)
- Chiara Regondi
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133, Milan, Italy.
| | - Maddalena Fratelli
- Pharmacogenomics Unit, Istituto di Ricerche Farmacologiche Mario Negri, IRCCS, 20156, Milan, Italy
| | - Giovanna Damia
- Laboratory of Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri, IRCCS, 20156, Milan, Italy
| | - Federica Guffanti
- Laboratory of Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri, IRCCS, 20156, Milan, Italy
| | - Monica Ganzinelli
- Laboratory of Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri, IRCCS, 20156, Milan, Italy.,Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133, Milan, Italy
| | - Matteo Matteucci
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133, Milan, Italy
| | - Marco Masseroli
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133, Milan, Italy
| |
Collapse
|
10
|
Tanoli Z, Aldahdooh J, Alam F, Wang Y, Seemab U, Fratelli M, Pavlis P, Hajduch M, Bietrix F, Gribbon P, Zaliani A, Hall MD, Shen M, Brimacombe K, Kulesskiy E, Saarela J, Wennerberg K, Vähä-Koskela M, Tang J. Minimal information for chemosensitivity assays (MICHA): a next-generation pipeline to enable the FAIRification of drug screening experiments. Brief Bioinform 2021; 23:6361039. [PMID: 34472587 PMCID: PMC8769689 DOI: 10.1093/bib/bbab350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 06/11/2021] [Revised: 08/03/2021] [Accepted: 08/02/2021] [Indexed: 12/29/2022] Open
Abstract
Chemosensitivity assays are commonly used for preclinical drug discovery and clinical trial optimization. However, data from independent assays are often discordant, largely attributed to uncharacterized variation in the experimental materials and protocols. We report here the launching of Minimal Information for Chemosensitivity Assays (MICHA), accessed via https://micha-protocol.org. Distinguished from existing efforts that are often lacking support from data integration tools, MICHA can automatically extract publicly available information to facilitate the assay annotation including: 1) compounds, 2) samples, 3) reagents and 4) data processing methods. For example, MICHA provides an integrative web server and database to obtain compound annotation including chemical structures, targets and disease indications. In addition, the annotation of cell line samples, assay protocols and literature references can be greatly eased by retrieving manually curated catalogues. Once the annotation is complete, MICHA can export a report that conforms to the FAIR principle (Findable, Accessible, Interoperable and Reusable) of drug screening studies. To consolidate the utility of MICHA, we provide FAIRified protocols from five major cancer drug screening studies as well as six recently conducted COVID-19 studies. With the MICHA web server and database, we envisage a wider adoption of a community-driven effort to improve the open access of drug sensitivity assays.
Collapse
Affiliation(s)
- Ziaurrehman Tanoli
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| | - Jehad Aldahdooh
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| | - Farhan Alam
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| | - Yinyin Wang
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| | - Umair Seemab
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| | | | - Petr Pavlis
- Institute of Molecular and Translational Medicine, Czech
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Czech
| | | | - Philip Gribbon
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Germany
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, USA
| | - Min Shen
- National Center for Advancing Translational Sciences, USA
| | | | - Evgeny Kulesskiy
- Institute for Molecular Medicine Finland, University of Helsinki, Finland
| | - Jani Saarela
- Institute for Molecular Medicine Finland, University of Helsinki, Finland
| | - Krister Wennerberg
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Denmark
| | | | - Jing Tang
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| |
Collapse
|
11
|
Tanoli Z, Aldahdooh J, Alam F, Wang Y, Seemab U, Fratelli M, Pavlis P, Hajduch M, Bietrix F, Gribbon P, Zaliani A, Hall MD, Shen M, Brimacombe K, Kulesskiy E, Saarela J, Wennerberg K, Vähä-Koskela M, Tang J. Minimal information for Chemosensitivity assays (MICHA): A next-generation pipeline to enable the FAIRification of drug screening experiments. bioRxiv 2021. [PMID: 33300000 PMCID: PMC7724669 DOI: 10.1101/2020.12.03.409409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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] [Indexed: 11/24/2022]
Abstract
Chemosensitivity assays are commonly used for preclinical drug discovery and clinical trial optimization. However, data from independent assays are often discordant, largely attributed to uncharacterized variation in the experimental materials and protocols. We report here the launching of MICHA (Minimal Information for Chemosensitivity Assays), accessed via https://micha-protocol.org. Distinguished from existing efforts that are often lacking support from data integration tools, MICHA can automatically extract publicly available information to facilitate the assay annotation including: 1) compounds, 2) samples, 3) reagents, and 4) data processing methods. For example, MICHA provides an integrative web server and database to obtain compound annotation including chemical structures, targets, and disease indications. In addition, the annotation of cell line samples, assay protocols and literature references can be greatly eased by retrieving manually curated catalogues. Once the annotation is complete, MICHA can export a report that conforms to the FAIR principle (Findable, Accessible, Interoperable and Reusable) of drug screening studies. To consolidate the utility of MICHA, we provide FAIRified protocols from five major cancer drug screening studies, as well as six recently conducted COVID-19 studies. With the MICHA webserver and database, we envisage a wider adoption of a community-driven effort to improve the open access of drug sensitivity assays.
Collapse
Affiliation(s)
- Ziaurrehman Tanoli
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| | - Jehad Aldahdooh
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| | - Farhan Alam
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| | - Yinyin Wang
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| | - Umair Seemab
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| | | | - Petr Pavlis
- Institute of Molecular and Translational Medicine, Czech
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Czech
| | | | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology, Hamburg, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology, Hamburg, Germany
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, U.S.A
| | - Min Shen
- National Center for Advancing Translational Sciences, U.S.A
| | | | - Evgeny Kulesskiy
- Institute for Molecular Medicine Finland, University of Helsinki, Finland
| | - Jani Saarela
- Institute for Molecular Medicine Finland, University of Helsinki, Finland
| | - Krister Wennerberg
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Denmark
| | | | - Jing Tang
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| |
Collapse
|
12
|
Abstract
Cancer is a complex disease characterized by a wide array of mutually interacting components constituting the tumor microenvironment (connective tissue, vascular system, immune cells), many of which are targeted therapeutically. In particular, immune checkpoint inhibitors have recently become an established part of the treatment of cancer. Despite great promise, only a portion of the patients display durable response. Current research efforts are concentrated on the determination of tumor-specific biomarkers predictive of response, such as tumor mutational burden, microsatellite instability, and neo-antigen presentation. However, it is clear that several additional characteristics pertaining to the tumor microenvironment play a critical role in the effectiveness of immunotherapy. Here we comment on the computational methods that are used for the analysis of the tumor microenvironment components from transcriptomic data, discuss the critical needs, and foresee potential evolutions in the field.
Collapse
Affiliation(s)
- Marco Bolis
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Arianna Vallerga
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | | |
Collapse
|
13
|
Castrignanò T, Gioiosa S, Flati T, Cestari M, Picardi E, Chiara M, Fratelli M, Amente S, Cirilli M, Tangaro MA, Chillemi G, Pesole G, Zambelli F. ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community. BMC Bioinformatics 2020; 21:352. [PMID: 32838759 PMCID: PMC7446135 DOI: 10.1186/s12859-020-03565-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The advent of Next Generation Sequencing (NGS) technologies and the concomitant reduction in sequencing costs allows unprecedented high throughput profiling of biological systems in a cost-efficient manner. Modern biological experiments are increasingly becoming both data and computationally intensive and the wealth of publicly available biological data is introducing bioinformatics into the "Big Data" era. For these reasons, the effective application of High Performance Computing (HPC) architectures is becoming progressively more recognized also by bioinformaticians. Here we describe HPC resources provisioning pilot programs dedicated to bioinformaticians, run by the Italian Node of ELIXIR (ELIXIR-IT) in collaboration with CINECA, the main Italian supercomputing center. RESULTS Starting from April 2016, CINECA and ELIXIR-IT launched the pilot Call "ELIXIR-IT HPC@CINECA", offering streamlined access to HPC resources for bioinformatics. Resources are made available either through web front-ends to dedicated workflows developed at CINECA or by providing direct access to the High Performance Computing systems through a standard command-line interface tailored for bioinformatics data analysis. This allows to offer to the biomedical research community a production scale environment, continuously updated with the latest available versions of publicly available reference datasets and bioinformatic tools. Currently, 63 research projects have gained access to the HPC@CINECA program, for a total handout of ~ 8 Millions of CPU/hours and, for data storage, ~ 100 TB of permanent and ~ 300 TB of temporary space. CONCLUSIONS Three years after the beginning of the ELIXIR-IT HPC@CINECA program, we can appreciate its impact over the Italian bioinformatics community and draw some considerations. Several Italian researchers who applied to the program have gained access to one of the top-ranking public scientific supercomputing facilities in Europe. Those investigators had the opportunity to sensibly reduce computational turnaround times in their research projects and to process massive amounts of data, pursuing research approaches that would have been otherwise difficult or impossible to undertake. Moreover, by taking advantage of the wealth of documentation and training material provided by CINECA, participants had the opportunity to improve their skills in the usage of HPC systems and be better positioned to apply to similar EU programs of greater scale, such as PRACE. To illustrate the effective usage and impact of the resources awarded by the program - in different research applications - we report five successful use cases, which have already published their findings in peer-reviewed journals.
Collapse
Affiliation(s)
- Tiziana Castrignanò
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy.
| | - Silvia Gioiosa
- CINECA, SuperComputing Applications and Innovation Department, Rome, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (IBIOM-CNR), Bari, Italy
| | - Tiziano Flati
- CINECA, SuperComputing Applications and Innovation Department, Rome, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (IBIOM-CNR), Bari, Italy
| | - Mirko Cestari
- CINECA, SuperComputing Applications and Innovation Department, Rome, Italy
| | - Ernesto Picardi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (IBIOM-CNR), Bari, Italy.,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
| | - Matteo Chiara
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (IBIOM-CNR), Bari, Italy.,Department of Biosciences, University of Milan, Milan, Italy
| | - Maddalena Fratelli
- IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Milan, Italy
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples 'Federico II', Naples, Italy
| | - Marco Cirilli
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy (DISAA), University of Milan, Milan, Italy
| | - Marco Antonio Tangaro
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (IBIOM-CNR), Bari, Italy
| | - Giovanni Chillemi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (IBIOM-CNR), Bari, Italy.,Department for Innovation in Biological, Agro-food and Forest systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (IBIOM-CNR), Bari, Italy. .,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy.
| | - Federico Zambelli
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (IBIOM-CNR), Bari, Italy. .,Department of Biosciences, University of Milan, Milan, Italy.
| |
Collapse
|
14
|
Bolis M, Paroni G, Fratelli M, Vallerga A, Guarrera L, Zanetti A, Kurosaki M, Garattini SK, Gianni’ M, Lupi M, Pattini L, Barzago MM, Terao M, Garattini E. All-Trans Retinoic Acid Stimulates Viral Mimicry, Interferon Responses and Antigen Presentation in Breast-Cancer Cells. Cancers (Basel) 2020; 12:cancers12051169. [PMID: 32384653 PMCID: PMC7281473 DOI: 10.3390/cancers12051169] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 04/01/2020] [Revised: 04/27/2020] [Accepted: 05/02/2020] [Indexed: 12/16/2022] Open
Abstract
All-trans retinoic acid (ATRA), a recognized differentiating agent, has significant potential in the personalized/stratified treatment of breast cancer. The present study reports on the molecular mechanisms underlying the anti-tumor activity of ATRA in breast cancer. The work is based on transcriptomic experiments performed on ATRA-treated breast cancer cell-lines, short-term tissue cultures of patient-derived mammary-tumors and a xenograft model. ATRA upregulates gene networks involved in interferon-responses, immune-modulation and antigen-presentation in retinoid-sensitive cells and tumors characterized by poor immunogenicity. ATRA-dependent upregulation of these gene networks is caused by a viral mimicry process, involving the activation of endogenous retroviruses. ATRA induces a non-canonical type of viral mimicry, which results in increased expression of the IRF1 (Interferon Responsive Factor 1) transcription factor and the DTX3L (Deltex-E3-Ubiquitin-Ligase-3L) downstream effector. Functional knockdown studies indicate that IRF1 and DTX3L are part of a negative feedback loop controlling ATRA-dependent growth inhibition of breast cancer cells. The study is of relevance from a clinical/therapeutic perspective. In fact, ATRA stimulates processes controlling the sensitivity to immuno-modulatory drugs, such as immune-checkpoint-inhibitors. This suggests that ATRA and immunotherapeutic agents represent rational combinations for the personalized treatment of breast cancer. Remarkably, ATRA-sensitivity seems to be relatively high in immune-cold mammary tumors, which are generally resistant to immunotherapy.
Collapse
Affiliation(s)
- Marco Bolis
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
- Functional Cancer Genomics Laboratory, Institute of Oncology Research, USI, University of Southern Switzerland, 6500 Bellinzona, Switzerland
- Bioinformatics Core Unit Institute of Oncology Research, Swiss Institute of Bioinformatics, 1000 Lausanne, Switzerland
| | - Gabriela Paroni
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
| | - Maddalena Fratelli
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
| | - Arianna Vallerga
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
| | - Luca Guarrera
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
| | - Adriana Zanetti
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
| | - Mami Kurosaki
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
| | - Silvio Ken Garattini
- Department of Oncology, Azienda Ospedaliera di Udine, DAME, Dipartimento di Area Medica Università degli Studi di Udine, 33100 Udine, Italy;
| | - Maurizio Gianni’
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
| | - Monica Lupi
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156 Milano, Italy;
| | - Linda Pattini
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, 20156 Milano, Italy;
| | - Maria Monica Barzago
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
| | - Mineko Terao
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
| | - Enrico Garattini
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
- Correspondence: ; Tel.: +39-02-3901-4533
| |
Collapse
|
15
|
Ricci F, Guffanti F, Affatato R, Brunelli L, Roberta P, Fruscio R, Perego P, Bani MR, Chiorino G, Rinaldi A, Bertoni F, Fratelli M, Damia G. Establishment of patient-derived tumor xenograft models of mucinous ovarian cancer. Am J Cancer Res 2020; 10:572-580. [PMID: 32195028 PMCID: PMC7061742] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/05/2019] [Indexed: 06/10/2023] Open
Abstract
Mucinous ovarian carcinoma (mEOC) represents a rare subtype of epithelial ovarian cancer, accounting for 3-4% of all ovarian carcinomas. The rarity of this tumor type renders both the preclinical and clinical research compelling. Very few preclinical in vitro and in vivo models exist. We here report the molecular, metabolic and pharmacological characterization of two patient derived xenografts (PDXs) from mEOC, recently obtained in our laboratory. These PDXs maintain the histological and molecular characteristics of the patient's tumors they derived from, including a wild type TP53. Gene expression analysis and metabolomics profile suggest that they differ from high grade serous/endometrioid ovarian carcinoma PDXs. The pharmacological characterization was undertaken testing the in vivo antitumor activity of both cytotoxic agents (cisplatin, paclitaxel, yondelis, oxaliplatin and 5-fluorouracile) and targeted agents (bevacizumab and lapatinib). These newly established mucinous PDXs do recapitulate mEOC and will be of value in the preclinical development of possible new therapeutic strategies for this tumor type.
Collapse
Affiliation(s)
- Francesca Ricci
- Laboratory of Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCSMilan 20156, Italy
| | - Federica Guffanti
- Laboratory of Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCSMilan 20156, Italy
| | - Roberta Affatato
- Laboratory of Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCSMilan 20156, Italy
| | - Laura Brunelli
- Protein and Gene Biomarkers Unit, Laboratory of Mass Spectrometry, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCSMilan 20156, Italy
| | - Pastorelli Roberta
- Protein and Gene Biomarkers Unit, Laboratory of Mass Spectrometry, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCSMilan 20156, Italy
| | - Robert Fruscio
- Clinic of Obstetrics and Gynecology, Department of Medicine and Surgery, San Gerardo Hospital, University of Milan BicoccaMonza 20900, Italy
| | - Patrizia Perego
- Clinic of Obstetrics and Gynecology, San Gerardo HospitalMonza 20900, Italy
| | - Maria Rosa Bani
- Laboratory of Laboratory of Biology and Treatment of Metastasis, Istituto di Ricerche Farmacologiche Mario Negri IRCCSMilan 20156, Italy
| | - Giovanna Chiorino
- Cancer Genomics Laboratory, Fondazione Edo and Elvo TempiaBiella, Italy
| | - Andrea Rinaldi
- Institute of Oncology Research, Università della Svizzera italianaBellinzona 6500, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Università della Svizzera italianaBellinzona 6500, Switzerland
| | - Maddalena Fratelli
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCSMilan 20156, Italy
| | - Giovanna Damia
- Laboratory of Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCSMilan 20156, Italy
| |
Collapse
|
16
|
Terao M, Goracci L, Celestini V, Kurosaki M, Bolis M, Di Veroli A, Vallerga A, Fratelli M, Lupi M, Corbelli A, Fiordaliso F, Gianni M, Paroni G, Zanetti A, Cruciani G, Garattini E. Correction to: Role of mitochondria and cardiolipins in growth inhibition of breast cancer cells by retinoic acid. J Exp Clin Cancer Res 2019; 38:496. [PMID: 31847869 PMCID: PMC6918558 DOI: 10.1186/s13046-019-1485-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Mineko Terao
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy.,Consortium for Computational Molecular and Materials Sciences (CMS), via Elce di Sotto 8, 06123, Perugia, Italy
| | - Valentina Celestini
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Mami Kurosaki
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Marco Bolis
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Alessandra Di Veroli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy
| | - Arianna Vallerga
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Maddalena Fratelli
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Monica Lupi
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Alessandro Corbelli
- Department of Cardiovascular Research, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Fabio Fiordaliso
- Department of Cardiovascular Research, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Maurizio Gianni
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Gabriela Paroni
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Adriana Zanetti
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy.,Consortium for Computational Molecular and Materials Sciences (CMS), via Elce di Sotto 8, 06123, Perugia, Italy
| | - Enrico Garattini
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy.
| |
Collapse
|
17
|
Terao M, Goracci L, Celestini V, Kurosaki M, Bolis M, Di Veroli A, Vallerga A, Fratelli M, Lupi M, Corbelli A, Fiordaliso F, Gianni M, Paroni G, Zanetti A, Cruciani G, Garattini E. Role of mitochondria and cardiolipins in growth inhibition of breast cancer cells by retinoic acid. J Exp Clin Cancer Res 2019; 38:436. [PMID: 31665044 PMCID: PMC6821005 DOI: 10.1186/s13046-019-1438-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 08/02/2019] [Accepted: 10/02/2019] [Indexed: 12/11/2022]
Abstract
Background All-trans-retinoic-acid (ATRA) is a promising agent in the prevention/treatment of breast-cancer. There is growing evidence that reprogramming of cellular lipid metabolism contributes to malignant transformation and progression. Lipid metabolism is implicated in cell differentiation and metastatic colonization and it is involved in the mechanisms of sensitivity/resistance to different anti-tumor agents. The role played by lipids in the anti-tumor activity of ATRA has never been studied. Methods We used 16 breast cancer cell-lines whose degree of sensitivity to the anti-proliferative action of ATRA is known. We implemented a non-oriented mass-spectrometry based approach to define the lipidomic profiles of each cell-line grown under basal conditions and following treatment with ATRA. To complement the lipidomic data, untreated and retinoid treated cell-lines were also subjected to RNA-sequencing to define the perturbations afforded by ATRA on the whole-genome gene-expression profiles. The number and functional activity of mitochondria were determined in selected ATRA-sensitive and –resistant cell-lines. Bio-computing approaches were used to analyse the high-throughput lipidomic and transcriptomic data. Results ATRA perturbs the homeostasis of numerous lipids and the most relevant effects are observed on cardiolipins, which are located in the mitochondrial inner membranes and play a role in oxidative-phosphorylation. ATRA reduces the amounts of cardiolipins and the effect is associated with the growth-inhibitory activity of the retinoid. Down-regulation of cardiolipins is due to a reduction of mitochondria, which is caused by an ATRA-dependent decrease in the expression of nuclear genes encoding mitochondrial proteins. This demonstrates that ATRA anti-tumor activity is due to a decrease in the amounts of mitochondria causing deficits in the respiration/energy-balance of breast-cancer cells. Conclusions The observation that ATRA anti-proliferative activity is caused by a reduction in the respiration and energy balance of the tumor cells has important ramifications for the therapeutic action of ATRA in breast cancer. The study may open the way to the development of rational therapeutic combinations based on the use of ATRA and anti-tumor agents targeting the mitochondria.
Collapse
Affiliation(s)
- Mineko Terao
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy.,Consortium for Computational Molecular and Materials Sciences (CMS), via Elce di Sotto 8, 06123, Perugia, Italy
| | - Valentina Celestini
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Mami Kurosaki
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Marco Bolis
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Alessandra Di Veroli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy
| | - Arianna Vallerga
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Maddalena Fratelli
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Monica Lupi
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Alessandro Corbelli
- Department of Cardiovascular Research, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Fabio Fiordaliso
- Department of Cardiovascular Research, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Maurizio Gianni
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Gabriela Paroni
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Adriana Zanetti
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy.,Consortium for Computational Molecular and Materials Sciences (CMS), via Elce di Sotto 8, 06123, Perugia, Italy
| | - Enrico Garattini
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156, Milan, Italy.
| |
Collapse
|
18
|
Ricci F, Brunelli L, Affatato R, Chilà R, Verza M, Indraccolo S, Falcetta F, Fratelli M, Fruscio R, Pastorelli R, Damia G. Overcoming platinum-acquired resistance in ovarian cancer patient-derived xenografts. Ther Adv Med Oncol 2019; 11:1758835919839543. [PMID: 31258626 PMCID: PMC6591669 DOI: 10.1177/1758835919839543] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 08/14/2018] [Accepted: 02/11/2019] [Indexed: 12/11/2022] Open
Abstract
Background: Epithelial ovarian cancer is the most lethal gynecological cancer and the
high mortality is due to the frequent presentation at advanced stage, and to
primary or acquired resistance to platinum-based therapy. Methods: We developed three new models of ovarian cancer patient-derived xenografts
(ovarian PDXs) resistant to cisplatin (cDDP) after multiple in
vivo drug treatments. By different and complementary approaches
based on integrated metabolomics (both targeted and untargeted mass
spectrometry-based techniques), gene expression, and functional assays
(Seahorse technology) we analyzed and compared the tumor metabolic profile
in each sensitive and their corresponding cDDP-resistant PDXs. Results: We found that cDDP-sensitive and -resistant PDXs have a different metabolic
asset. In particular, we found, through metabolomic and gene expression
approaches, that glycolysis, tricarboxylic acid cycle and urea cycle
pathways were deregulated in resistant versus sensitive
PDXs. In addition, we observed that oxygen consumption rate and
mitochondrial respiration were higher in resistant PDXs than in sensitive
PDXs under acute stress conditions. An increased oxidative phosphorylation
in cDDP-resistant sublines led us to hypothesize that its interference could
be of therapeutic value. Indeed, in vivo treatment of
metformin and cDDP was able to partially reverse platinum resistance. Conclusions: Our data strongly reinforce the idea that the development of acquired cDDP
resistance in ovarian cancer can bring about a rewiring of tumor metabolism,
and that this might be exploited therapeutically.
Collapse
Affiliation(s)
- Francesca Ricci
- Department of Oncology, Laboratory of Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Laura Brunelli
- Department of Environmental Health Sciences, Laboratory of Mass Spectometry, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Roberta Affatato
- Department of Oncology, Laboratory of Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Rosaria Chilà
- Department of Oncology, Laboratory of Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Martina Verza
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV-IRCCS, Padova, Italy
| | - Stefano Indraccolo
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV-IRCCS, Padova, Italy
| | | | | | - Robert Fruscio
- Department of Medicine and Surgery, University of Milan Bicocca, 20900, Monza, Italy
| | - Roberta Pastorelli
- Department of Environmental Health Sciences, Laboratory of Mass Spectometry, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Giovanna Damia
- Department of Oncology, Laboratory of Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| |
Collapse
|
19
|
Paroni G, Zanetti A, Bolis M, Vallerga A, Troiani M, Fratelli M, Kurosaki M, Terao M, Garattini E. Abstract P5-05-08: Molecular cross-talk between retinoic acid and NOTCH1 signaling pathways: Role in triple negative breast cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p5-05-08] [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
Triple Negative Breast Cancer (TNBC) represents 10-20% of all breast cancers and it is characterized by poor prognosis and high recurrence rate. The heterogeneity of the disease and the absence of well-defined molecular targets have so far challenged successful therapeutic strategies. NOTCH1 has been found to act as a driver oncogene in a small subset of TNBC characterized by constitutive activation of the protein, acting as a transcription factor. Preclinical studies support an anti-tumor activity of All-Trans Retinoic Acid (ATRA) in specific subsets of breast cancer.
By screening a large panel of breast cancer cell lines recapitulating the heterogeneity of TNBC we identify a specific subset sensitive to the anti-proliferative activity of ATRA. These cell lines (N-TNBC cell lines) are characterized by a Notch1 intragenic fusion transcript conferring gain of function activity to the protein. Indeed, sequence analysis reveals that the cell lines harbor an interstitial deletion in the NOTCH1 gene encompassing the negative regulatory region (NRR) domain. These cell lines depend on Notch active signaling for their proliferation since their cell growth is impaired by Notch inhibitors (γ-secretase inhibitors, e.g. DAPT, PF-3084014). Proliferation assays reveal that ATRA and γ-secretase inhibitors act synergistically in inhibiting cancer cell growth in N-TNBC cell lines suggesting the existence of a cross talk between the molecular pathways engaged by retinoic acid and NOTCH1.
By using retinoic acid receptors (RARs) agonists and antagonists as well as RAR specific silencing experiments we identify RARα as the retinoic acid receptor responsible of the anti-proliferation activity of ATRA in N-TNBC cell lines. In particular N-TNBC cell lines respond to RARα activation by inducing high amounts of the onco-supressor protein RARβ. This feature is unique in ATRA sensitive TNBC cell lines and does not occur in ATRA sensitive luminal cell lines arguing for the existence of a retinoic acid specific mechanism of action in N-TNBC. Since RARs act as transcription factors inside the cells, to gain insights into the molecular pathway at the basis of the observed ATRA/NOTCH1 cross talk, we performed RNAseq analysis of ATRA and/or DAPT treated N-TNBC cells. Gene set enrichment analysis reveal that ATRA is able to directly affect NOTCH1 transduction pathway by modulating the expression of NOTCH1 target genes. In particular, in two out of three N-TNBC cell lines ATRA directly inhibits the NOTCH1 expression at a transcriptional level and its downregulation is increased by ATRA/DAPT combinations. Pathway analysis has allowed the identification of putative molecular hubs responsible for the synergistic effects observed and therefore likely at the basis of the crosstalk between ATRA/NOTCH pathways. These findings are of clinical interest since both the retinoid and NOTCH signaling display crucial physiologic activities and their pleiotropic effects could impinge on the success of therapeutic options based on their pathway modulation.
The newly discovered specificity of ATRA action in the context of NOTCH1 addicted TNBC provides new tools for the identification of patients candidates benefitting from strategies targeting the ATRA/NOTCH axis.
Citation Format: Paroni G, Zanetti A, Bolis M, Vallerga A, Troiani M, Fratelli M, Kurosaki M, Terao M, Garattini E. Molecular cross-talk between retinoic acid and NOTCH1 signaling pathways: Role in triple negative breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-05-08.
Collapse
Affiliation(s)
- G Paroni
- Mario Negri Institute for Pharmacological Research, Milan, Italy
| | - A Zanetti
- Mario Negri Institute for Pharmacological Research, Milan, Italy
| | - M Bolis
- Mario Negri Institute for Pharmacological Research, Milan, Italy
| | - A Vallerga
- Mario Negri Institute for Pharmacological Research, Milan, Italy
| | - M Troiani
- Mario Negri Institute for Pharmacological Research, Milan, Italy
| | - M Fratelli
- Mario Negri Institute for Pharmacological Research, Milan, Italy
| | - M Kurosaki
- Mario Negri Institute for Pharmacological Research, Milan, Italy
| | - M Terao
- Mario Negri Institute for Pharmacological Research, Milan, Italy
| | - E Garattini
- Mario Negri Institute for Pharmacological Research, Milan, Italy
| |
Collapse
|
20
|
Terao M, Celestini V, Kurosaki M, Vallerga A, Bolis M, Fratelli M, Paroni G, Di Veroli A, Cruciani G, Goracci L, Garattini E. Abstract P2-02-15: All-trans retinoic acid perturbs the lipidomic profiles of luminal breast cancer cells characterized by sensitivity to the anti-proliferative activity of the retinoid. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p2-02-15] [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
Background: All-trans retinoic acid (ATRA) is the active metabolite of vitamin A and a promising agent in the prevention and treatment of breast cancer. We recently demonstrated that approximately 70% of estrogen-receptor-positive (ER+) breast cancer cell lines and primary tumors are sensitive to the anti-proliferative effects of ATRA (1,2). In contrast only 10-20% of the HER2-positive and triple-negative counterparts respond to the retinoid. The significance of lipids in the growth, progression and drug sensitivity of specific types of solid tumors, including breast cancer, is largely overlooked. In particular the role, if any, of specific lipids in the anti-tumor action of ATRA in breast cancer has never been studied.
Aims and Approach: The principal aim of the present work was to evaluate the specific perturbations induced by ATRA on the homeostasis of lipids in breast cancer cells characterized by sensitivity to the anti-proliferative action of the retinoid. To this purpose, we took a high-throughput approach and defined the lipidomic profiles of 16 breast cancer cell lines in basal conditions and following challenge with ATRA (1 μM) for 48 hours. The panel consisted of eight cell lines characterized by a luminal phenotype and eight cell lines with a basal phenotype. Four ATRA-sensitive cell lines (SKBR3, HCC1500, CAMA1 and MDAMB361) and 4 ATRA-resistant counterparts (HCC202, MDAMB175VII, ZR75.1 and HCC1419) were included in the luminal group. Similarly, the basal group contained 4 ATRA-sensitive (HCC1599, MB157, MDAMB157 and Hs578T) and 4 ATRA-resistant (MDAMB231, CAL851, HCC1187 and MDAMB436) cell types.
Results: Using Lipostar, a unique and recently developed software for high-throughput LC-MS lipidomics analysis (3), we identified lipid species whose levels were modified by ATRA in each cell line. This resulted in the generation of a lipid fingerprint consisting of 530 elements. We observed that ATRA reduced the amounts of cardiolipins in luminal and ATRA-sensitive breast cancer cell lines specifically. Similar effects were not observed in luminal and ATRA-resistant cells. ATRA-dependent reduction in the amounts of cardiolipins were never observed in basal cells, regardless of their sensitivity to the retinoid. Given the role played by cardiolipins in the homeostasis of the mitochondria, we evaluated the action of ATRA on the functional activity of these organelles in the luminal and ATRA-sensitive or ATRA-resistant cell lines. In SKBR3 and the other sensitive cell lines, we observed that ATRA modulated mitochondria-dependent oxygen consumption and ATP production. These effects were accompanied by an increase in mitochondrial membrane fluidity, which is consistent with the effects exerted by ATRA on the cellular content of cardiolipins. ATRA-dependent action on cardiolipins and mitochondrial homeostasis precedes maximal growth inhibition. The results provide new insights on the mechanisms underlying the anti-tumor action of ATRA.
References : 1) Centritto F. et al. EMBO Mol Med. 2015 Jul;7(7):950-72. 2) Bolis M et al.. Ann Oncol. 2017 Mar 1;28(3):611-621. 3) Goracci, L. et al., Anal Chem 2017, 89 (11), 6258-6265.
Citation Format: Terao M, Celestini V, Kurosaki M, Vallerga A, Bolis M, Fratelli M, Paroni G, Di Veroli A, Cruciani G, Goracci L, Garattini E. All-trans retinoic acid perturbs the lipidomic profiles of luminal breast cancer cells characterized by sensitivity to the anti-proliferative activity of the retinoid [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-02-15.
Collapse
Affiliation(s)
- M Terao
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy; University of Perugia, Perugia, Italy
| | - V Celestini
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy; University of Perugia, Perugia, Italy
| | - M Kurosaki
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy; University of Perugia, Perugia, Italy
| | - A Vallerga
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy; University of Perugia, Perugia, Italy
| | - M Bolis
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy; University of Perugia, Perugia, Italy
| | - M Fratelli
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy; University of Perugia, Perugia, Italy
| | - G Paroni
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy; University of Perugia, Perugia, Italy
| | - A Di Veroli
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy; University of Perugia, Perugia, Italy
| | - G Cruciani
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy; University of Perugia, Perugia, Italy
| | - L Goracci
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy; University of Perugia, Perugia, Italy
| | - E Garattini
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy; University of Perugia, Perugia, Italy
| |
Collapse
|
21
|
Garattini E, Bolis M, Vallerga A, Fratelli M, Paroni G, Zanetti A, Kurosaki M, Gianni' M, Celestini V, Terao M. Abstract P5-05-09: Systemic perturbations induced by all-trans retinoic acid in the gene-expression profiles of sixteen breast cancer cell lines characterized by sensitivity and resistance to the anti-proliferative effects of the retinoid. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p5-05-09] [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
Background: All-trans retinoic acid (ATRA) is a promising agent in the treatment of breast cancer. In view of ATRA-based therapeutic strategies aimed at the personalized treatment of mammary tumors, we recently demonstrated that approximately 70% of estrogen-receptor-positive (ER+) breast cancer is sensitive to the anti-proliferative effects of ATRA (1). In contrast only 10-20% of the HER2-positive and triple-negative counterparts respond to the retinoid. On the basis of these data and the available basal gene-expression profiles of breast cancer cell lines and primary tumors, we developed a model consisting of 21 genes (ATRA-21) which correctly predicts ATRA-sensitivity in the context of breast cancer (2).
Aims and Approach: The present study is aimed at getting insights into the molecular mechanisms underlying the anti-tumor action of ATRA in the specific subsets of breast cancer identified. In addition, we intend to determine specific genes and gene-networks modulated by ATRA which may represent pharmacological targets for the design of rational combinations between the retinoid and unrelated therapeutic agents to be used in the personalized treatment of breast cancer. A final goal is the identification of potential bio-markers of the anti-tumor response to ATRA to be used in the clinics. To address all these points, we performed deep-sequencing experiments on a panel of sixteen cell lines recapitulating the heterogeneity of the breast cancer phenotype and characterized for their anti-proliferative response to ATRA.
Panel of Breast cancer cell lines and characteristicsCell linePhenotypeClassATRA-scoreATRA-sensitivitySKBR3LUMINALHER2+1.0yesHCC1500LUMINALER+0.7yesCAMA1LUMINALER+0.7yesMDAMB361LUMINALHER2+0.6yesHCC202LUMINALHER2+0.2noMDAMB175VIILUMINALER+0.2noZR751LUMINALER+0.1noHCC1419LUMINALHER2+0.1noHCC1599BASALTN1.0yesMB157BASALTN0.3yesMDAMB157BASALTN0.2yesHS578TBASALTN0.2yesMDAMB231BASALTN0.0noCAL851BASALTN0.0noHCC1187BASALTN0.0noMDAMB436BASALTN0.0noATRA-score = ATRA sensitivity index, the higher the score the higher is the sensitivity to ATRA. ER+ = estrogen-receptor-positive cell line. HER2+ = Her2-positive cell line.
Results: We exposed each cell line to ATRA (1 μM) for 24 hours and extracted total RNA which was subjected to deep sequencing. The global gene-expression data were analyzed with a number of complementary bio-informatic tools which resulted in the identification of approximately 100 genes whose expression is up- or down-regulated specifically in ATRA-sensitive luminal and/or basal cell lines. Pathway and gene-network analysis indicate a strong enrichment in the up-regulation of genes involved in the pathways modulated by interferons. These last results are consistent with the idea that ATRA exerts a strong immuno-modulatory action in breast cancer cells and represents proof of principle for the evaluation of combinations between the retinoid and check-point inhibitors in the treatment of breast cancer.
References: 1) Centritto F. et al. EMBO Mol Med. 2015 Jul;7(7):950-7. 2) Bolis M et al.. Ann Oncol. 2017 Mar 1;28(3):611-621.
Citation Format: Garattini E, Bolis M, Vallerga A, Fratelli M, Paroni G, Zanetti A, Kurosaki M, Gianni' M, Celestini V, Terao M. Systemic perturbations induced by all-trans retinoic acid in the gene-expression profiles of sixteen breast cancer cell lines characterized by sensitivity and resistance to the anti-proliferative effects of the retinoid [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-05-09.
Collapse
Affiliation(s)
- E Garattini
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - M Bolis
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - A Vallerga
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - M Fratelli
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - G Paroni
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - A Zanetti
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - M Kurosaki
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - M Gianni'
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - V Celestini
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - M Terao
- Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| |
Collapse
|
22
|
Paroni G, Bolis M, Zanetti A, Ubezio P, Helin K, Staller P, Gerlach LO, Fratelli M, Neve RM, Terao M, Garattini E. HER2-positive breast-cancer cell lines are sensitive to KDM5 inhibition: definition of a gene-expression model for the selection of sensitive cases. Oncogene 2018; 38:2675-2689. [DOI: 10.1038/s41388-018-0620-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/09/2018] [Accepted: 11/19/2018] [Indexed: 12/31/2022]
|
23
|
Gioiosa S, Bolis M, Flati T, Massini A, Garattini E, Chillemi G, Fratelli M, Castrignanò T. Massive NGS data analysis reveals hundreds of potential novel gene fusions in human cell lines. Gigascience 2018; 7:5026623. [PMID: 29860514 PMCID: PMC6207142 DOI: 10.1093/gigascience/giy062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 09/22/2017] [Accepted: 05/29/2018] [Indexed: 01/19/2023] Open
Abstract
Background Gene fusions derive from chromosomal rearrangements. The resulting chimeric transcripts are often endowed with oncogenic potential. Furthermore, they serve as diagnostic tools for the clinical classification of cancer subgroups with different prognosis and, in some cases, they can provide specific drug targets. To date, many efforts have been carried out to study gene fusion events occurring in tumor samples. In recent years, the availability of a comprehensive next-generation sequencing dataset for all existing human tumor cell lines has provided the opportunity to further investigate these data in order to identify novel and still uncharacterized gene fusion events. Results In our work, we have extensively reanalyzed 935 paired-end RNA-sequencing experiments downloaded from the Cancer Cell Line Encyclopedia repository, aiming at addressing novel putative cell-line specific gene fusion events in human malignancies. The bioinformatics analysis has been performed by the execution of four gene fusion detection algorithms. The results have been further prioritized by running a Bayesian classifier that makes an in silico validation. The collection of fusion events supported by all of the predictive software results in a robust set of ∼1,700 in silico predicted novel candidates suitable for downstream analyses. Given the huge amount of data and information produced, computational results have been systematized in a database named LiGeA. The database can be browsed through a dynamic and interactive web portal, further integrated with validated data from other well-known repositories. Taking advantage of the intuitive query forms, the users can easily access, navigate, filter, and select the putative gene fusions for further validations and studies. They can also find suitable experimental models for a given fusion of interest. Conclusions We believe that the LiGeA resource can represent not only the first compendium of both known and putative novel gene fusion events in the catalog of all of the human malignant cell lines but it can also become a handy starting point for wet-lab biologists who wish to investigate novel cancer biomarkers and specific drug targets.
Collapse
Affiliation(s)
- Silvia Gioiosa
- SCAI-Super Computing Applications and Innovation Department, CINECA, Rome, Italy.,National Council of Research, CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | - Marco Bolis
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri," Milano, Italy
| | - Tiziano Flati
- SCAI-Super Computing Applications and Innovation Department, CINECA, Rome, Italy.,National Council of Research, CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | | | - Enrico Garattini
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri," Milano, Italy
| | - Giovanni Chillemi
- SCAI-Super Computing Applications and Innovation Department, CINECA, Rome, Italy
| | - Maddalena Fratelli
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri," Milano, Italy
| | - Tiziana Castrignanò
- SCAI-Super Computing Applications and Innovation Department, CINECA, Rome, Italy
| |
Collapse
|
24
|
Guffanti F, Fratelli M, Ganzinelli M, Bolis M, Ricci F, Bizzaro F, Chilà R, Sina FP, Fruscio R, Lupia M, Cavallaro U, Cappelletti MR, Generali D, Giavazzi R, Damia G. Platinum sensitivity and DNA repair in a recently established panel of patient-derived ovarian carcinoma xenografts. Oncotarget 2018; 9:24707-24717. [PMID: 29872499 PMCID: PMC5973859 DOI: 10.18632/oncotarget.25185] [Citation(s) in RCA: 16] [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: 01/29/2018] [Accepted: 04/05/2018] [Indexed: 01/22/2023] Open
Abstract
A xenobank of patient-derived (PDX) ovarian tumor samples has been established consisting of tumors with different sensitivity to cisplatin (DDP), from very responsive to resistant. As the DNA repair pathway is an important driver in tumor response to DDP, we analyzed the mRNA expression of 20 genes involved in the nucleotide excision repair, fanconi anemia, homologous recombination, base excision repair, mismatch repair and translesion repair pathways and the methylation patterns of some of these genes. We also investigated the correlation with the response to platinum-based therapy. The mRNA levels of the selected genes were evaluated by Real Time-PCR (RT-PCR) with ad hoc validated primers and gene promoter methylation by pyrosequencing. All the DNA repair genes were variably expressed in all 42 PDX samples analyzed, with no particular histotype-specific pattern of expression. In high-grade serous/endometrioid PDXs, the CDK12 mRNA expression levels positively correlated with the expression of TP53BP1, PALB2, XPF and POLB. High-grade serous/endometrioid PDXs with TP53 mutations had significantly higher levels of POLQ, FANCD2, RAD51 and POLB than high-grade TP53 wild type PDXs. The mRNA levels of CDK12, PALB2 and XPF inversely associated with the in vivo DDP antitumor activity; higher CDK12 mRNA levels were associated with a higher recurrence rate in ovarian patients with low residual tumor. These data support the important role of CDK12 in the response to a platinum based therapy in ovarian patients.
Collapse
Affiliation(s)
- Federica Guffanti
- Department of Oncology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Maddalena Fratelli
- Department of Biochemistry, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Monica Ganzinelli
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Marco Bolis
- Department of Biochemistry, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Francesca Ricci
- Department of Oncology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Francesca Bizzaro
- Department of Oncology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Rosaria Chilà
- Department of Oncology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Federica Paola Sina
- Clinic of Obstetrics and Gynecology, San Gerardo Hospital, University of Milan-Bicocca, Department of Medicine and Surgery, Milan, Italy
| | - Robert Fruscio
- Clinic of Obstetrics and Gynecology, San Gerardo Hospital, University of Milan-Bicocca, Department of Medicine and Surgery, Milan, Italy
| | - Michela Lupia
- Unit of Gynecological Oncology Research, European Institute of Oncology, Milan, Italy
| | - Ugo Cavallaro
- Unit of Gynecological Oncology Research, European Institute of Oncology, Milan, Italy
| | | | - Daniele Generali
- Breast Cancer Unit and Translational Research Unit, ASST Cremona, Cremona, Italy.,Department of Medical, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Raffaella Giavazzi
- Department of Oncology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Giovanna Damia
- Department of Oncology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| |
Collapse
|
25
|
Gianni M, Fratelli M, Bolis M, Kurosaki M, Zanetti A, Paroni G, Rambaldi A, Borleri G, Rochette-Egly C, Terao M, Garattini E. RARα2 and PML-RAR similarities in the control of basal and retinoic acid induced myeloid maturation of acute myeloid leukemia cells. Oncotarget 2018; 8:37041-37060. [PMID: 27419624 PMCID: PMC5514891 DOI: 10.18632/oncotarget.10556] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 05/16/2016] [Accepted: 07/01/2016] [Indexed: 02/02/2023] Open
Abstract
Treatment of acute promyelocytic leukemia (APL) with all-trans retinoic acid (ATRA) is the first example of targeted therapy. In fact, the oncogenic fusion-protein (PML-RAR) typical of this leukemia contains the retinoid-nuclear-receptor RARα. PML-RAR is responsible for the differentiation block of the leukemic blast. Besides PML-RAR, two endogenous RARα proteins are present in APL blasts, i.e. RARα1 and RARα2. We developed different cell populations characterized by PML-RAR, RARα2 and RARα1 knock-down in the APL-derived NB4 cell-line. Unexpectedly, silencing of PML-RAR and RARα2 results in similar increases in the constitutive expression of several granulocytic differentiation markers. This is accompanied by enhanced expression of the same granulocytic markers upon exposure of the NB4 blasts to ATRA. Silencing of PML-RAR and RARα2 causes also similar perturbations in the whole genome gene-expression profiles of vehicle and ATRA treated NB4 cells. Unlike PML-RAR and RARα2, RARα1 knock-down blocks ATRA-dependent induction of several granulocytic differentiation markers. Many of the effects on myeloid differentiation are confirmed by over-expression of RARα2 in NB4 cells. RARα2 action on myeloid differentiation does not require the presence of PML-RAR, as it is recapitulated also upon knock-down in PML-RAR-negative HL-60 cells. Thus, relative to RARα1, PML-RAR and RARα2 exert opposite effects on APL-cell differentiation. These contrasting actions may be related to the fact that both PML-RAR and RARα2 interact with and inhibit the transcriptional activity of RARα1. The interaction surface is located in the carboxy-terminal domain containing the D/E/F regions and it is influenced by phosphorylation of Ser-369 of RARα1.
Collapse
Affiliation(s)
- Maurizio Gianni
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", 20156 Milano, Italy
| | - Maddalena Fratelli
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", 20156 Milano, Italy
| | - Marco Bolis
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", 20156 Milano, Italy
| | - Mami Kurosaki
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", 20156 Milano, Italy
| | - Adriana Zanetti
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", 20156 Milano, Italy
| | - Gabriela Paroni
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", 20156 Milano, Italy
| | - Alessandro Rambaldi
- Hematology and Bone Marrow Transplant Unit, Azienda Ospedaliera Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Gianmaria Borleri
- Hematology and Bone Marrow Transplant Unit, Azienda Ospedaliera Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Cecile Rochette-Egly
- Department of Functional Genomics and Cancer, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM, U964, CNRS, UMR7104, Université de Strasbourg, 67404 Illkirch Cedex, France
| | - Mineko Terao
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", 20156 Milano, Italy
| | - Enrico Garattini
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", 20156 Milano, Italy
| |
Collapse
|
26
|
Ricci F, Fratelli M, Guffanti F, Porcu L, Spriano F, Dell'Anna T, Fruscio R, Damia G. Patient-derived ovarian cancer xenografts re-growing after a cisplatinum treatment are less responsive to a second drug re-challenge: a new experimental setting to study response to therapy. Oncotarget 2018; 8:7441-7451. [PMID: 26910918 PMCID: PMC5352333 DOI: 10.18632/oncotarget.7465] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 10/05/2015] [Accepted: 02/05/2016] [Indexed: 02/06/2023] Open
Abstract
Even if ovarian cancer patients are very responsive to a cisplatinum-based therapy, most will relapse with a resistant disease. New experimental animal models are needed to explore the mechanisms of resistance, to better tailor treatment and improve patient prognosis. To address these aims, seven patient-derived high-grade serous/endometrioid ovarian cancer xenografts were characterized for the antitumor response after one and two cycles of cisplatinum and classified as Very Responsive, Responsive, and Low Responsive to drug treatment. Xenografts re-growing after the first drug cycle were much less responsive to the second one. The expression of epithelial-mesenchymal transition (EMT) and cancer stem cells (CSCs) genes was investigated in cisplatinum-treated and not-treated tumors. We found that different EMT (TCF3, CAMK2N1, EGFR, and IGFBP4) and CSCs (SMO, DLL1, STAT3, and ITGA6) genes were expressed at higher levels in Low Responsive than in Responsive and Very Responsive xenografts. The expression of STAT3 was found to be associated with lower survival (HR = 13.7; p = 0.013) in the TCGA patient data set. MMP9, CD44, DLL4, FOXP1, MERTK, and PTPRC genes were found more expressed in tumors re-growing after cisplatinum treatment than in untreated tumors. We here describe a new in vivo ovarian carcinoma experimental setting that will be instrumental for specific trials of combination therapy to counteract cisplatinum resistance in order to improve the prognosis of ovarian patients.
Collapse
Affiliation(s)
- Francesca Ricci
- Department of Oncology, Laboratory of Molecular Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Maddalena Fratelli
- Department of Biochemistry, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Federica Guffanti
- Department of Oncology, Laboratory of Molecular Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Luca Porcu
- Department of Oncology, Laboratory of Methodology for Biomedical Research, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Filippo Spriano
- Department of Oncology, Laboratory of Molecular Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Tiziana Dell'Anna
- Obstetrics and Gynecology Clinic, San Gerardo Hospital, Monza, Italy
| | - Robert Fruscio
- Obstetrics and Gynecology Clinic, San Gerardo Hospital, Monza, Italy
| | - Giovanna Damia
- Department of Oncology, Laboratory of Molecular Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| |
Collapse
|
27
|
Bolis M, Garattini E, Paroni G, Zanetti A, Kurosaki M, Castrignanò T, Garattini SK, Biancardi F, Barzago MM, Gianni' M, Terao M, Pattini L, Fratelli M. Network-guided modeling allows tumor-type independent prediction of sensitivity to all-trans-retinoic acid. Ann Oncol 2017; 28:611-621. [PMID: 27993792 DOI: 10.1093/annonc/mdw660] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background All-trans-retinoic acid (ATRA) is a differentiating agent used in the treatment of acute-promyelocytic-leukemia (APL) and it is under-exploited in other malignancies despite its low systemic toxicity. A rational/personalized use of ATRA requires the development of predictive tools allowing identification of sensitive cancer types and responsive individuals. Materials and methods RNA-sequencing data for 10 080 patients and 33 different tumor types were derived from the TCGA and Leucegene datasets and completely re-processed. The study was carried out using machine learning methods and network analysis. Results We profiled a large panel of breast-cancer cell-lines for in vitro sensitivity to ATRA and exploited the associated basal gene-expression data to initially generate a model predicting ATRA-sensitivity in this disease. Starting from these results and using a network-guided approach, we developed a generalized model (ATRA-21) whose validity extends to tumor types other than breast cancer. ATRA-21 predictions correlate with experimentally determined sensitivity in a large panel of cell-lines representative of numerous tumor types. In patients, ATRA-21 correctly identifies APL as the most sensitive acute-myelogenous-leukemia subtype and indicates that uveal-melanoma and low-grade glioma are top-ranking diseases as for average predicted responsiveness to ATRA. There is a consistent number of tumor types for which higher ATRA-21 predictions are associated with better outcomes. Conclusions In summary, we generated a tumor-type independent ATRA-sensitivity predictor which consists of a restricted number of genes and has the potential to be applied in the clinics. Identification of the tumor types that are likely to be generally sensitive to the action of ATRA paves the way to the design of clinical studies in the context of these diseases. In addition, ATRA-21 may represent an important diagnostic tool for the selection of individual patients who may benefit from ATRA-based therapeutic strategies also in tumors characterized by lower average sensitivity.
Collapse
Affiliation(s)
- M Bolis
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milano.,Department of Electronics, Information and Bioengineering, Politecnico di Milano, Milano
| | - E Garattini
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milano
| | - G Paroni
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milano
| | - A Zanetti
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milano
| | - M Kurosaki
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milano
| | - T Castrignanò
- Computing Centre, CINECA-Consorzio Interuniversitario per il Calcolo Automatico, Roma
| | - S K Garattini
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milano.,Department of Medical Oncology, University Hospital, Udine, Italy
| | - F Biancardi
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milano
| | - M M Barzago
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milano
| | - M Gianni'
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milano
| | - M Terao
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milano
| | - L Pattini
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Milano
| | - M Fratelli
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milano
| |
Collapse
|
28
|
Barzago MM, Kurosaki M, Fratelli M, Bolis M, Giudice C, Nordio L, Cerri E, Domenici L, Terao M, Garattini E. Generation of a new mouse model of glaucoma characterized by reduced expression of the AP-2β and AP-2δ proteins. Sci Rep 2017; 7:11140. [PMID: 28894266 PMCID: PMC5593953 DOI: 10.1038/s41598-017-11752-6] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 08/30/2017] [Indexed: 12/20/2022] Open
Abstract
We generated 6 transgenic lines with insertion of an expression plasmid for the R883/M xanthine dehydrogenase (XDH) mutant protein. Approximately 20% of the animals deriving from one of the transgenic lines show ocular abnormalities and an increase in intra-ocular pressure which are consistent with glaucoma. The observed pathologic phenotype is not due to expression of the transgene, but rather the consequence of the transgene insertion site, which has been defined by genome sequencing. The insertion site maps to chromosome 1qA3 in close proximity to the loci encoding AP-2β and AP-2δ, two proteins expressed in the eye. The insertion leads to a reduction in AP-2β and AP-2δ levels. Down-regulation of AP-2β expression is likely to be responsible for the pathologic phenotype, as conditional deletion of the Tfap2b gene in the neural crest has recently been shown to cause defective development of the eye anterior segment and early-onset glaucoma. In these conditional knock-out and our transgenic mice, the morphological/histological features of the glaucomatous pathology are surprisingly similar. Our transgenic mouse represents a model of angle-closure glaucoma and a useful tool for the study of the pathogenesis and the development of innovative therapeutic strategies.
Collapse
Affiliation(s)
- Maria Monica Barzago
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Mami Kurosaki
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Maddalena Fratelli
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Marco Bolis
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Chiara Giudice
- DIVET, Faculty of Veterinary Medicine, University of Milan, Italy, Via Celoria 10, 20113, Milano, Italy
| | - Laura Nordio
- DIVET, Faculty of Veterinary Medicine, University of Milan, Italy, Via Celoria 10, 20113, Milano, Italy
| | - Elisa Cerri
- Consiglio Nazionale delle Ricerche (CNR), Neuroscience Institute, Pisa, Italy
| | - Luciano Domenici
- Consiglio Nazionale delle Ricerche (CNR), Neuroscience Institute, Pisa, Italy
- Department of Applied Clinical Sciences and Biotechnology (DISCAB), University of L'Aquila, L'Aquila, Italy
| | - Mineko Terao
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy.
| | - Enrico Garattini
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy.
| |
Collapse
|
29
|
Garattini E, Bolis M, Fratelli M, Terao M. Abstract 5543: Network guided modeling allows tumor type independent prediction of sensitivity to retinoic acid. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-5543] [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
Background: All-trans retinoic acid (ATRA) is a differentiating agent used in the treatment of acute-promyelocytic-leukemia and it is under-exploited in other malignancies despite its low systemic toxicity. A rational/personalized use of ATRA requires development of predictive tools allowing identification of sensitive cancer types and responsive individuals.
Materials and Methods: RNA-Sequencing data for 10080 patients and 33 different tumor-types were derived from the TCGA and Leucegene datasets and completely re-processed. The study was performed using machine learning methods and network analysis.
Results: We profiled a large panel of breast-cancer cell-lines for in vitro sensitivity to ATRA and exploited the associated basal gene-expression data to initially generate a model predicting ATRA-sensitivity in this disease. Starting from these results and using a network-guided approach, we developed a generalized model (ATRA-21) whose validity extends to tumor-types other than breast cancer. ATRA-21 predictions correlate with experimentally determined sensitivity in a large panel of cell-lines representative of numerous tumor-types. In patients, ATRA-21 correctly identifies APL as the most sensitive acute-myelogenous-leukemia subtype and indicates that uveal-melanoma and low-grade glioma are top-ranking diseases as for average predicted responsiveness to ATRA. There is a consistent number of tumor-types for which higher ATRA-21 predictions are associated with better outcomes.
Conclusions: In summary, we generated a tumor-type independent ATRA-sensitivity predictor which consists of a restricted number of genes and has the potential to be applied in the clinics. Identification of the tumor-types which are likely to be generally sensitive to the action of ATRA paves the way to the design of clinical studies in the context of these diseases. In addition, ATRA-21 may represent an important diagnostic tool for the selection of individual patients who may benefit from ATRA-based therapeutic strategies also in tumors characterized by lower average sensitivity.
Citation Format: Enrico Garattini, Marco Bolis, Maddalena Fratelli, Mineko Terao. Network guided modeling allows tumor type independent prediction of sensitivity to retinoic acid [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5543. doi:10.1158/1538-7445.AM2017-5543
Collapse
Affiliation(s)
| | - Marco Bolis
- Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | | | - Mineko Terao
- Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| |
Collapse
|
30
|
Guffanti F, Fratelli M, Ganzinelli M, Ricci F, Affatato R, Cappelletti MR, Generali D, Bizzaro F, Broggini M, Giavazzi R, Damia G. Abstract 508: DNA repair status in a patient derived ovarian cancer xenobank. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-508] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Epithelial ovarian cancer (EOC) is the most lethal gynecological malignancy with a 5-year relative survival rate of 45%. The high mortality rate is in part due to the development of platinum chemoresistance occurring in more than 70% of patients after the first-line therapy. DNA repair capacity has been reported to be a key determinant for the cellular response to platinum agents. Since half of the high grade serous EOCs lacks Homologous Recombination repair, we aimed to profile the DNA repair status in a panel of well characterized 42 ovarian patient derived xenografts (PDXs) recently established in our laboratory and to correlate it with the in vivo response to a platinum based therapy. We evaluated by real time PCR (ABI-7900, Applied Biosystems) the mRNA levels of genes with a key role in Base Excision Repair (OGG1, POLB and PARP1), Homologous Recombination (BRCA1, PALB2, TP53BP1 and RAD51), Nucleotide Excision Repair (ERCC1, XPA, XPF, XPD and XPG), Fanconi Anemia pathway (FANCA, FANCC, FANCD2 and FANCF), Translesion Repair (POLEta), Mismatch Repair (MLH1), Microhomology End Joining (POLQ), Non Homologous End Joining (XRCC4, XRCC5, XRCC6 and XRCC7) and CDK12, a kinase regulating the transcription of some DNA repair genes. The methylation status of BRCA1, ERCC1, MLH1, XPA, XPG and FANCF was investigated by standard techniques. Our results show that the DNA repair genes considered were variably expressed in all the 42 PDXs analyzed, with no specific histotype-specific cluster of expression. The expression of PALB2, FANCC, FANCD2, OGG1, POLQ and RAD51 was found to correlate with the expression of at least six other genes. In high grade serous/endometrioid PDXs, the CDK12 mRNA expression levels positively correlated with the expression of TP53BP1, PALB2, XPF and POLB. BRCA1 was found to be hypermethylated in 51% of the xenografts. TP53 mutated PDXs showed statistically significant higher levels of POLQ, FANCD2, RAD51, and POLB genes. The expression of CDK12 [p=0.017], PALB2 [p=0.019] and XPF [p= 0.016] was negatively associated with the in vivo response to DDP, with resistant PDXs showing higher mRNA levels than responsive ones. We looked for association with overall survival in the TCGA data set and we found that high levels of CDK12 were associated with a worse overall survival in patients with a residual tumor after surgery minus than 2cm. These data suggest that some DNA repair genes can have a role in EOC patients’ response to DDP therapy. Particularly, CDK12 was significantly able to predict worse survival in patients undergoing optimal debulking surgery. Our xenobank will be a valid instrument to set up functional DNA repair assays, as suggested by preliminary data on primary cultures.
Citation Format: Federica Guffanti, Maddalena Fratelli, Monica Ganzinelli, Francesca Ricci, Roberta Affatato, Maria Rosa Cappelletti, Daniele Generali, Francesca Bizzaro, Massimo Broggini, Raffaella Giavazzi, Giovanna Damia. DNA repair status in a patient derived ovarian cancer xenobank [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 508. doi:10.1158/1538-7445.AM2017-508
Collapse
Affiliation(s)
- Federica Guffanti
- 1IRCCS - Institute for Pharmacological Research Mario Negri, Milan, Italy
| | - Maddalena Fratelli
- 1IRCCS - Institute for Pharmacological Research Mario Negri, Milan, Italy
| | - Monica Ganzinelli
- 1IRCCS - Institute for Pharmacological Research Mario Negri, Milan, Italy
| | - Francesca Ricci
- 1IRCCS - Institute for Pharmacological Research Mario Negri, Milan, Italy
| | - Roberta Affatato
- 1IRCCS - Institute for Pharmacological Research Mario Negri, Milan, Italy
| | | | - Daniele Generali
- 2Azienda Socio-Sanitaria Territoriale di Cremona, Cremona, Italy
| | - Francesca Bizzaro
- 1IRCCS - Institute for Pharmacological Research Mario Negri, Milan, Italy
| | - Massimo Broggini
- 1IRCCS - Institute for Pharmacological Research Mario Negri, Milan, Italy
| | - Raffaella Giavazzi
- 1IRCCS - Institute for Pharmacological Research Mario Negri, Milan, Italy
| | - Giovanna Damia
- 1IRCCS - Institute for Pharmacological Research Mario Negri, Milan, Italy
| |
Collapse
|
31
|
Terao M, Barzago MM, Kurosaki M, Fratelli M, Bolis M, Borsotti A, Bigini P, Micotti E, Carli M, Invernizzi RW, Bagnati R, Passoni A, Pastorelli R, Brunelli L, Toschi I, Cesari V, Sanoh S, Garattini E. Mouse aldehyde-oxidase-4 controls diurnal rhythms, fat deposition and locomotor activity. Sci Rep 2016; 6:30343. [PMID: 27456060 PMCID: PMC4960552 DOI: 10.1038/srep30343] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 11/26/2015] [Accepted: 06/30/2016] [Indexed: 02/03/2023] Open
Abstract
Aldehyde-oxidase-4 (AOX4) is one of the mouse aldehyde oxidase isoenzymes and its physiological function is unknown. The major source of AOX4 is the Harderian-gland, where the enzyme is characterized by daily rhythmic fluctuations. Deletion of the Aox4 gene causes perturbations in the expression of the circadian-rhythms gene pathway, as indicated by transcriptomic analysis. AOX4 inactivation alters the diurnal oscillations in the expression of master clock-genes. Similar effects are observed in other organs devoid of AOX4, such as white adipose tissue, liver and hypothalamus indicating a systemic action. While perturbations of clock-genes is sex-independent in the Harderian-gland and hypothalamus, sex influences this trait in liver and white-adipose-tissue which are characterized by the presence of AOX isoforms other than AOX4. In knock-out animals, perturbations in clock-gene expression are accompanied by reduced locomotor activity, resistance to diet induced obesity and to hepatic steatosis. All these effects are observed in female and male animals. Resistance to obesity is due to diminished fat accumulation resulting from increased energy dissipation, as white-adipocytes undergo trans-differentiation towards brown-adipocytes. Metabolomics and enzymatic data indicate that 5-hydroxyindolacetic acid and tryptophan are novel endogenous AOX4 substrates, potentially involved in AOX4 systemic actions.
Collapse
Affiliation(s)
- Mineko Terao
- Laboratory of Molecular Biology, Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Maria Monica Barzago
- Laboratory of Molecular Biology, Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Mami Kurosaki
- Laboratory of Molecular Biology, Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Maddalena Fratelli
- Laboratory of Molecular Biology, Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Marco Bolis
- Laboratory of Molecular Biology, Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Andrea Borsotti
- Laboratory of Molecular Biology, Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Paolo Bigini
- Laboratory of Biochemistry and Protein Chemistry, Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Edoardo Micotti
- Laboratory of Neurodegenerative diseases, Department of Neuroscience, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Mirjana Carli
- Laboratory of Neurochemistry and Behaviour, Department of Neuroscience, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Roberto William Invernizzi
- Laboratory of Neurochemistry and Behaviour, Department of Neuroscience, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Renzo Bagnati
- Analytical Instrumentation Unit, Department of Environmental Health Sciences, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Alice Passoni
- Analytical Instrumentation Unit, Department of Environmental Health Sciences, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Roberta Pastorelli
- Laboratory of Mass Spectrometry, Department of Environmental Health Sciences; IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Laura Brunelli
- Laboratory of Mass Spectrometry, Department of Environmental Health Sciences; IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Ivan Toschi
- Department of Agricultural and Environmental Sciences; Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Valentina Cesari
- Department of Agricultural and Environmental Sciences; Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Seigo Sanoh
- Graduate School of Biochemical and Health Sciences, Hiroshima University, Hiroshima Japan
| | - Enrico Garattini
- Laboratory of Molecular Biology, Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| |
Collapse
|
32
|
Garattini E, Gianni’ M, Bolis M, Fratelli M, Paroni G, Terao M. Abstract 2101: A gene-expression fingerprint predicting sensitivity to all-trans-retinoic acid in breast cancer cells is tumor-context independent. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2101] [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
All-trans retinoic acid (ATRA) and derived natural as well as synthetic retinoids are promising agents in the treatment and chemoprevention of various types of neoplasia, including mammary tumors. ATRA is an important component of the therapeutic schemes used for the treatment of a rare form of Acute Myelogenous Leukemia known as Acute Promyelocytic Leukemia (APL). A rational use of the paradigmatic retinoid, ATRA, in a heterogeneous disease, like breast cancer, requires the definition of the cellular and molecular determinants of sensitivity to the agent. The major aim of the study was the definition of a predictive gene expression fingerprint that can be used for the selection of patients who may benefit from treatment protocols containing ATRA. To this purpose, we selected 53 breast cancer cell lines characterized for the constitutive whole genome gene expression profiles. The sensitivity of 30 cell lines (training set) to the anti-proliferative action of ATRA was defined after challenge with increasing concentrations of the retinoid for 3, 6 and 9 days. This analysis established that Luminal and ER+ cell lines are enriched within the ATRA sensitive group. In contrast, cell lines characterized by a Basal-like phenotype, according to the PAM50 gene expression signature, are generally refractory to the growth inhibitory action of ATRA. The sensitivity of Luminal-A and Luminal-B and the general refractoriness of Basal-like tumors to ATRA was validated in short-term tissue slice cultures of surgical breast cancer specimens. The training set was used to define a gene-expression fingerprint consisting of morethan 100 genes significantly associated with ATRA sensitivity. The fingerprint was generated by reprocessing the RNA sequencing data contained in the CCLE (Cancer Cell line Encyclopedia) of the Broad Institute and it was built from approximately 60,000 coding and non-coding loci. The approach involved the use of general linear models (machine learning algorithm). The identified gene-expression fingerprint was subsequently used to successfully predict ATRA sensitivity in a test set consisting of the remaining 23 cell lines. As a first step towards the use of the fingerprint for the stratification of patients, we evaluated the proportion of predicted ATRA sensitive breast tumors in the TCGA dataset. In accordance with the cell line and primary tumor data, approximately 30% of the Luminal tumors present with a high similarity score to the identified gene expression fingerprint associated with ATRA sensitivity. In contrast, only 5% of the Basal-like or Triple-negative mammary tumors are characterized by the same high similarity score. Interestingly, the ATRA sensitivity signature seems to be tumor context independent, as it correctly identifies the Acute Promyelocytic Leukemia patients present in the Acute Myelogenous Leukemia patients present in two publicly available datasets.
Citation Format: Enrico Garattini, Maurizio Gianni’, Marco Bolis, Maddalena Fratelli, Gabriela Paroni, Mineko Terao. A gene-expression fingerprint predicting sensitivity to all-trans-retinoic acid in breast cancer cells is tumor-context independent. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2101.
Collapse
Affiliation(s)
| | | | - Marco Bolis
- Mario Negri Inst. for Pharmacol. Research, Milan, Italy
| | | | | | - Mineko Terao
- Mario Negri Inst. for Pharmacol. Research, Milan, Italy
| |
Collapse
|
33
|
Centritto F, Paroni G, Bolis M, Garattini SK, Kurosaki M, Barzago MM, Zanetti A, Fisher JN, Scott MF, Pattini L, Lupi M, Ubezio P, Piccotti F, Zambelli A, Rizzo P, Gianni' M, Fratelli M, Terao M, Garattini E. Cellular and molecular determinants of all-trans retinoic acid sensitivity in breast cancer: Luminal phenotype and RARα expression. EMBO Mol Med 2016; 7:950-72. [PMID: 25888236 PMCID: PMC4520659 DOI: 10.15252/emmm.201404670] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [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] [Indexed: 01/26/2023] Open
Abstract
Forty-two cell lines recapitulating mammary carcinoma heterogeneity were profiled for all-trans retinoic acid (ATRA) sensitivity. Luminal and ER+ (estrogen-receptor-positive) cell lines are generally sensitive to ATRA, while refractoriness/low sensitivity is associated with a Basal phenotype and HER2 positivity. Indeed, only 2 Basal cell lines (MDA-MB157 and HCC-1599) are highly sensitive to the retinoid. Sensitivity of HCC-1599 cells is confirmed in xenotransplanted mice. Short-term tissue-slice cultures of surgical samples validate the cell-line results and support the concept that a high proportion of Luminal/ER+ carcinomas are ATRA sensitive, while triple-negative (Basal) and HER2-positive tumors tend to be retinoid resistant. Pathway-oriented analysis of the constitutive gene-expression profiles in the cell lines identifies RARα as the member of the retinoid pathway directly associated with a Luminal phenotype, estrogen positivity and ATRA sensitivity. RARα3 is the major transcript in ATRA-sensitive cells and tumors. Studies in selected cell lines with agonists/antagonists confirm that RARα is the principal mediator of ATRA responsiveness. RARα over-expression sensitizes retinoid-resistant MDA-MB453 cells to ATRA anti-proliferative action. Conversely, silencing of RARα in retinoid-sensitive SKBR3 cells abrogates ATRA responsiveness. All this is paralleled by similar effects on ATRA-dependent inhibition of cell motility, indicating that RARα may mediate also ATRA anti-metastatic effects. We define gene sets of predictive potential which are associated with ATRA sensitivity in breast cancer cell lines and validate them in short-term tissue cultures of Luminal/ER+ and triple-negative tumors. In these last models, we determine the perturbations in the transcriptomic profiles afforded by ATRA. The study provides fundamental information for the development of retinoid-based therapeutic strategies aimed at the stratified treatment of breast cancer subtypes.
Collapse
Affiliation(s)
- Floriana Centritto
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
| | - Gabriela Paroni
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
| | - Marco Bolis
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
| | - Silvio Ken Garattini
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
| | - Mami Kurosaki
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
| | - Maria Monica Barzago
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
| | - Adriana Zanetti
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
| | - James Neil Fisher
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
| | - Mark Francis Scott
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
| | - Linda Pattini
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Milan, Italy
| | - Monica Lupi
- Department of Oncology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
| | - Paolo Ubezio
- Department of Oncology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
| | | | | | - Paola Rizzo
- Gene Therapy and Cellular Reprogramming, IRCCS- Istituto di Ricerche Farmacologiche "Mario Negri", Bergamo, Italy
| | - Maurizio Gianni'
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
| | - Maddalena Fratelli
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
| | - Mineko Terao
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
| | - Enrico Garattini
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
| |
Collapse
|
34
|
Fratelli M, Bolis M, Kurosaki M, Dori M, Guarnaccia V, Spinelli O, Alberti M, Valoti E, Pileggi S, Noris M, Remuzzi G, Rambaldi A, Terao M, Garattini E. Association of CFHR1 homozygous deletion with acute myelogenous leukemia in the European population. Leuk Lymphoma 2016; 57:1234-7. [PMID: 26317246 DOI: 10.3109/10428194.2015.1082180] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Maddalena Fratelli
- a Laboratory of Molecular Biology , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156 , Milano , Italy
| | - Marco Bolis
- a Laboratory of Molecular Biology , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156 , Milano , Italy
| | - Mami Kurosaki
- a Laboratory of Molecular Biology , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156 , Milano , Italy
| | - Martina Dori
- a Laboratory of Molecular Biology , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156 , Milano , Italy
| | - Valeria Guarnaccia
- a Laboratory of Molecular Biology , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156 , Milano , Italy
| | - Orietta Spinelli
- b Division of Hematology , Azienda Ospedaliera Papa Giovanni XXIII , Bergamo , Italy
| | - Marta Alberti
- c Immunology and Genetics of Rare Diseases and Organ Transplantation, Clinical Research Center for Rare Diseases "Aldo & Cele Daccò" , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri" , Ranica (BG) , Italy
| | - Elisabetta Valoti
- c Immunology and Genetics of Rare Diseases and Organ Transplantation, Clinical Research Center for Rare Diseases "Aldo & Cele Daccò" , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri" , Ranica (BG) , Italy
| | - Silvana Pileggi
- d Laboratory of Clinical Drug Evaluation , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri" , Milano , Italy
| | - Marina Noris
- c Immunology and Genetics of Rare Diseases and Organ Transplantation, Clinical Research Center for Rare Diseases "Aldo & Cele Daccò" , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri" , Ranica (BG) , Italy
| | - Giuseppe Remuzzi
- e Clinical Research Center for Rare Diseases "Aldo & Cele Daccò" , Ranica (BG) , Italy ;,f Centro Anna Maria Astori , Science and Technology Park Kilometro Rosso , Bergamo , Italy ; and.,g IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri" and Unit of Nephrology , Azienda Ospedaliera Papa Giovanni XXIII , Bergamo , Italy
| | - Alessandro Rambaldi
- b Division of Hematology , Azienda Ospedaliera Papa Giovanni XXIII , Bergamo , Italy
| | - Mineko Terao
- a Laboratory of Molecular Biology , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156 , Milano , Italy
| | - Enrico Garattini
- a Laboratory of Molecular Biology , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156 , Milano , Italy
| |
Collapse
|
35
|
Garattini E, Bolis M, Paroni G, Fratelli M, Zambelli A, Terao M. Abstract P6-04-09: Cellular and molecular determinants of breast cancer sensitivity to all-trans retinoic acid: Identification of a gene expression fingerprint predicting responsiveness. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p6-04-09] [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
All-trans retinoic acid (ATRA) and derived natural as well as synthetic retinoids are promising agents in the treatment and chemoprevention of various types of neoplasia, including mammary tumors. ATRA is an important component of the therapeutic schemes used for the treatment of a rare form of Acute Myelogenous Leukemia known as Acute Promyelocytic Leukemia. A rational use of the paradigmatic retinoid, ATRA, in a heterogeneous disease, like breast cancer, requires the definition of the cellular and molecular determinants of sensitivity to the agent. The major aim of the study was the definition of a predictive gene expression fingerprint that can be used for the selection of patients who may benefit from treatment protocols containing ATRA. To this purpose, we selected 45 breast cancer cell lines characterized for the constitutive whole genome gene expression profiles. The sensitivity of 30 cell lines (training set) to the anti-proliferative action of ATRA was defined after challenge with increasing concentrations of the retinoid for 3, 6 and 9 days. This analysis established that Luminal and ER-positive cell lines are enriched within the ATRA sensitive group. In contrast, cell lines characterized by a Basal-like phenotype, according to the PAM50 gene expression signature, are generally refractory to the growth inhibitory action of ATRA. The sensitivity of Luminal-A and Luminal-B and the general refractoriness of Basal-like tumors to ATRA was validated in short-term tissue slice cultures of surgical breast cancer specimens. The training set was used to define a gene-expression fingerprint consisting of approximately 50 genes significantly associated with ATRA sensitivity. The fingerprint was generated by reprocessing the RNA sequencing data contained in the CCLE (Cancer Cell line Encyclopedia) of the Broad Institute and it was built from approximately 60,000 coding and non-coding loci. The approach involved the use of general linear models (machine learning algorithm). The identified gene-expression fingerprint was subsequently used to successfully predict ATRA sensitivity in a test set consisting of the remaining 15 cell lines. As a first step towards the use of the fingerprint for the stratification of patients, we evaluated the proportion of predicted ATRA sensitive breast tumors in the TCGA dataset. In accordance with the cell line and primary tumor data, approximately 30% of the Luminal tumors present with a high similarity score to the identified gene expression fingerprint associated with ATRA sensitivity. In contrast, only 5% of the Basal-like or Triple-negative mammary tumors are characterized by the same high similarity score. Curiously, the ATRA sensitivity signature seems to be tumor context independent, as it correctly identifies the 20 Acute Promyelocytic Leukemia patients present in the 198 Acute Myelogenous Leukemia patients present in the TCGA dataset.
Citation Format: Garattini E, Bolis M, Paroni G, Fratelli M, Zambelli A, Terao M. Cellular and molecular determinants of breast cancer sensitivity to all-trans retinoic acid: Identification of a gene expression fingerprint predicting responsiveness. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-04-09.
Collapse
Affiliation(s)
- E Garattini
- IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy; Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - M Bolis
- IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy; Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - G Paroni
- IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy; Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - M Fratelli
- IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy; Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - A Zambelli
- IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy; Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - M Terao
- IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy; Ospedale Papa Giovanni XXIII, Bergamo, Italy
| |
Collapse
|
36
|
Ricci F, Guffanti F, Fratelli M, Massimo B, Damia G. Abstract 4091: Investigations on the role of epithelial-mesenchymal transition and cancer stem cells in the response to therapy in patient-derived ovarian carcinoma xenografts. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-4091] [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
Epithelial ovarian cancer (EOC) has the highest mortality rate in the western world among gynaecological malignancies. Approximately 70% of patients achieve complete remission after first-line platinum-based therapy, but unfortunately, almost all patients relapse with the development of a resistant disease. Progress has been made in identifying “hallmarks” of cancer, and the epithelial-mesenchymal transition (EMT) and the presence of cancer stem cells (CSCs) have been associated with aggressiveness and chemoresistant properties.
These studies were designed to better understand the role of CSCs and EMT in the resistance to a platinum-based therapy in a panel of patient-derived ovarian carcinoma xenografts recently characterized (Ricci F et al, Cancer Res 2014). These xenografts reproduce the complexity and the heterogeneity of ovarian cancer both at a biological (i.e. histotypes, pattern of spread) and molecular levels (i.e. gene mutations and transcriptomic).
In order to investigate the role of EMT and CSC in ovarian cancer, 10 different ovarian carcinoma xenografts (4 serous, 3 endometrioid, 2 mucinous, and 1 müllerian-mixed tumor) were treated with cisplatinum (CDDP) once a week for 3 weeks at the dose of 5 mg/kg. Then, a second CDDP cycle was given to the regrowing tumors, mimicking clinical conditions. Ovarian xenografts showed different sensitivity to the first CDDP cycle, but almost all were less sensitive to the second CDDP cycle. Xenografts were classified as “Very Responsive” (VR), “Responsive” (R), and “Non-Responsive” (NR) on the basis of their therapy response. By RT-PCR (Qiagen, RT2 ProfilerTM PCR Array System) the expression of EMT and CSCs genes (n = 86 for each array) was evaluated in untreated and CDDP-treated xenografts. Statistical analysis were performed by using the Significance of Microarrays (SAM) method.
The expression of EMT genes supported the recently put forward idea that the different ovarian histotypes are to be considered as different diseases. Indeed, xenografts belonging to the same hystotype clustered in the same group. We then focus on the role of EMT genes in prediciting CDDP sensitivity in serous and endometroid carcinomas subtype. We found that transcription factor 3 (TCF3 gene) was more expressed in NR than in the VR and R xenografst, with a gradual increase among the 3 different groups starting from VR to NR xenografts. In addition, the upregulation of 3 genes (DSP, MITF, and WNT5B) was induced after CDDP treatment. Preliminary analysis on the same group of xenografts showed that CDDP treatment causes a modulation of CSC genes.
These new xenograft models will be instrumental in clarifying the role, if any, of EMT and CSCs in both predicting response to CDDP and in testing novel therapeutic strategies in ovarian carcinomas.
Citation Format: Francesca Ricci, Federica Guffanti, Maddalena Fratelli, Broggini Massimo, Giovanna Damia. Investigations on the role of epithelial-mesenchymal transition and cancer stem cells in the response to therapy in patient-derived ovarian carcinoma xenografts. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4091. doi:10.1158/1538-7445.AM2015-4091
Collapse
Affiliation(s)
| | | | | | | | - Giovanna Damia
- IRCCS- Istituto di Ricerche Farmacologiche, Milan, Italy
| |
Collapse
|
37
|
Zanetti A, Affatato R, Centritto F, Fratelli M, Kurosaki M, Barzago MM, Bolis M, Terao M, Garattini E, Paroni G. All-trans-retinoic Acid Modulates the Plasticity and Inhibits the Motility of Breast Cancer Cells: ROLE OF NOTCH1 AND TRANSFORMING GROWTH FACTOR (TGFβ). J Biol Chem 2015; 290:17690-17709. [PMID: 26018078 DOI: 10.1074/jbc.m115.638510] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [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: 01/14/2015] [Indexed: 01/06/2023] Open
Abstract
All-trans-retinoic acid (ATRA) is a natural compound proposed for the treatment/chemoprevention of breast cancer. Increasing evidence indicates that aberrant regulation of epithelial-to-mesenchymal transition (EMT) is a determinant of the cancer cell invasive and metastatic behavior. The effects of ATRA on EMT are largely unknown. In HER2-positive SKBR3 and UACC812 cells, showing co-amplification of the ERBB2 and RARA genes, ATRA activates a RARα-dependent epithelial differentiation program. In SKBR3 cells, this causes the formation/reorganization of adherens and tight junctions. Epithelial differentiation and augmented cell-cell contacts underlie the anti-migratory action exerted by the retinoid in cells exposed to the EMT-inducing factors EGF and heregulin-β1. Down-regulation of NOTCH1, an emerging EMT modulator, is involved in the inhibition of motility by ATRA. Indeed, the retinoid blocks NOTCH1 up-regulation by EGF and/or heregulin-β1. Pharmacological inhibition of γ-secretase and NOTCH1 processing also abrogates SKBR3 cell migration. Stimulation of TGFβ contributes to the anti-migratory effect of ATRA. The retinoid switches TGFβ from an EMT-inducing and pro-migratory determinant to an anti-migratory mediator. Inhibition of the NOTCH1 pathway not only plays a role in the anti-migratory action of ATRA; it is relevant also for the anti-proliferative activity of the retinoid in HCC1599 breast cancer cells, which are addicted to NOTCH1 for growth/viability. This effect is enhanced by the combination of ATRA and the γ-secretase inhibitor N-(N-(3,5-difluorophenacetyl)-l-alanyl)-S-phenylglycine t-butyl ester, supporting the concept that the two compounds act at the transcriptional and post-translational levels along the NOTCH1 pathway.
Collapse
Affiliation(s)
- Adriana Zanetti
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156 Milano, Italy
| | - Roberta Affatato
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156 Milano, Italy
| | - Floriana Centritto
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156 Milano, Italy
| | - Maddalena Fratelli
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156 Milano, Italy
| | - Mami Kurosaki
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156 Milano, Italy
| | - Maria Monica Barzago
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156 Milano, Italy
| | - Marco Bolis
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156 Milano, Italy
| | - Mineko Terao
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156 Milano, Italy
| | - Enrico Garattini
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156 Milano, Italy
| | - Gabriela Paroni
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156 Milano, Italy.
| |
Collapse
|
38
|
Garattini E, Centritto F, Garattini SK, Paroni G, Bolis M, Fratelli M, Terao M. Abstract 2099: Cellular and molecular determinants of retinoic acid sensitivity in breast cancer. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-2099] [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
All-trans-retinoic acid (ATRA) is the primary metabolite of vitamin A and a promising agent in the treatment/prevention of solid tumors, including breast cancer. Breast cancer is a very heterogeneous disease that can be classified according to the global gene-expression profiles into various subgroups. A rational use of ATRA in the clinics requires definition of the breast cancer subtypes characterized by sensitivity/natural-resistance to this compound and derived retinoids. In addition, it is fundamental to define the cellular and molecular mechanisms underlying the sensitivity/resistance to ATRA. As a first step in this direction, 44 breast cancer cell lines, belonging to the Cancer Cell Line Encyclopedia (CCLE) of the Broad Institute and recapitulating the heterogeneity of this tumor, were evaluated for their sensitivity to the anti-proliferative activity of ATRA. Individual cell lines were challenged with increasing concentrations of the retinoid for 3, 6 and 9 days. The concentrations of ATRA causing 50% of the maximal growth inhibition (IC50) and the maximal effect observed were calculated. The two parameters, along with the duplication time of the cell lines, were used to define a novel algorithm (ATRA SCORE). The ATRA score is a continuous parameter which defines the sensitivity of the cell lines to ATRA in a quantitative fashion. The lower the ATRA score the higher the sensitivity of the cell to the anti-proliferative action of ATRA. Using this score, an enrichment in cell lines characterized by a luminal phenotype and/or estrogen receptor (ER)-positivity was observed in the group showing sensitivity to ATRA. In contrast an enrichment in cell lines with a basal phenotype and/or ER-negativity was evident in the group characterized by natural resistance to the retinoid. Measurement of the mRNAs corresponding to various isoforms of the retinoid receptors belonging to the RAR and RXR family in the 44 cell lines allowed us to establish correlations between the expression of these transcripts and ATRA sensitivity. With respect to this, we found a significant and direct correlation with the expression levels of RARalpha1. This indicates that the receptor represents a determinant and a predictor of ATRA- sensitivity in breast cancer cells. The correlation was confirmed also at the protein level using specific RARalpha antibodies. Most of these findings were validated with the use of short-term cultures of breast cancer tissue slices obtained from surgical specimens. The availability of the global gene-expression profiles of each cell line permitted the construction of a gene fingerprint consisting of approximately 130 elements that has the potential to predict sensitivity to ATRA not only in breast cancer cell lines, but also in tumor samples. In addition, the identified gene fingerprint allowed the identification of various and unexpected molecular determinants of sensitivity which do not belong to the classic retinoid pathway.
Citation Format: Enrico Garattini, Floriana Centritto, Silvio K. Garattini, Gabriela Paroni, Marco Bolis, Maddalena Fratelli, Mineko Terao. Cellular and molecular determinants of retinoic acid sensitivity in breast cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2099. doi:10.1158/1538-7445.AM2014-2099
Collapse
Affiliation(s)
| | | | | | | | - Marco Bolis
- Mario Negri Institute for Pharmacol. Research, Milan, Italy
| | | | - Mineko Terao
- Mario Negri Institute for Pharmacol. Research, Milan, Italy
| |
Collapse
|
39
|
Ricci F, Guffanti F, Fratelli M, Perego P, Fruscio R, Baldo R, Magni S, Broggini M, Damia G. 601: Cisplatin response in a panel of patient-derived ovarian carcinoma xenografts: roles of epithelial mesenchymal transition and DNA repair. Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)50534-5] [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: 10/25/2022]
|
40
|
Finardi A, Colciaghi F, Castana L, Locatelli D, Marras CE, Nobili P, Fratelli M, Bramerio MA, Lorusso G, Battaglia GS. Long-duration epilepsy affects cell morphology and glutamatergic synapses in type IIB focal cortical dysplasia. Acta Neuropathol 2013; 126:219-35. [PMID: 23793416 DOI: 10.1007/s00401-013-1143-4] [Citation(s) in RCA: 22] [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: 03/18/2013] [Revised: 05/30/2013] [Accepted: 06/11/2013] [Indexed: 11/24/2022]
Abstract
To investigate hypothesized effects of severe epilepsy on malformed cortex, we analyzed surgical samples from eight patients with type IIB focal cortical dysplasia (FCD) in comparison with samples from nine non-dysplastic controls. We investigated, using stereological quantification methods, where appropriate, dysplastic neurons, neuronal density, balloon cells, glia, glutamatergic synaptic input, and the expression of N-methyl-D-aspartate (NMDA) receptor subunits and associated membrane-associated guanylate kinase (MAGUK). In all FCD patients, the dysplastic areas giving rise to epileptic discharges were characterized by larger dysmorphic neurons, reduced neuronal density, and increased glutamatergic inputs, compared to adjacent areas with normal cytology. The duration of epilepsy was found to correlate directly (a) with dysmorphic neuron size, (b) reduced neuronal cell density, and (c) extent of reactive gliosis in epileptogenic/dysplastic areas. Consistent with increased glutamatergic input, western blot revealed that NMDA regulatory subunits and related MAGUK proteins were up-regulated in epileptogenic/dysplastic areas of all FCD patients examined. Taken together, these results support the hypothesis that epilepsy itself alters morphology-and probably also function-in the malformed epileptic brain. They also suggest that glutamate/NMDA/MAGUK dysregulation might be the intracellular trigger that modifies brain morphology and induces cell death.
Collapse
Affiliation(s)
- Adele Finardi
- Experimental Neurophysiology and Epileptology Department, Molecular Neuroanatomy and Pathogenesis Unit, Neurological Institute C. Besta, Via Temolo 4, 20126, Milan, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Kurosaki M, Bolis M, Fratelli M, Barzago MM, Pattini L, Perretta G, Terao M, Garattini E. Structure and evolution of vertebrate aldehyde oxidases: from gene duplication to gene suppression. Cell Mol Life Sci 2013; 70:1807-30. [PMID: 23263164 PMCID: PMC11113236 DOI: 10.1007/s00018-012-1229-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [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: 08/04/2012] [Revised: 11/29/2012] [Accepted: 12/03/2012] [Indexed: 12/20/2022]
Abstract
Aldehyde oxidases (AOXs) and xanthine dehydrogenases (XDHs) belong to the family of molybdo-flavoenzymes. Although AOXs are not identifiable in fungi, these enzymes are represented in certain protists and the majority of plants and vertebrates. The physiological functions and substrates of AOXs are unknown. Nevertheless, AOXs are major drug metabolizing enzymes, oxidizing a wide range of aromatic aldehydes and heterocyclic compounds of medical/toxicological importance. Using genome sequencing data, we predict the structures of AOX genes and pseudogenes, reconstructing their evolution. Fishes are the most primitive organisms with an AOX gene (AOXα), originating from the duplication of an ancestral XDH. Further evolution of fishes resulted in the duplication of AOXα into AOXβ and successive pseudogenization of AOXα. AOXβ is maintained in amphibians and it is the likely precursors of reptilian, avian, and mammalian AOX1. Amphibian AOXγ is a duplication of AOXβ and the likely ancestor of reptilian and avian AOX2, which, in turn, gave rise to mammalian AOX3L1. Subsequent gene duplications generated the two mammalian genes, AOX3 and AOX4. The evolution of mammalian AOX genes is dominated by pseudogenization and deletion events. Our analysis is relevant from a structural point of view, as it provides information on the residues characterizing the three domains of each mammalian AOX isoenzyme. We cloned the cDNAs encoding the AOX proteins of guinea pig and cynomolgus monkeys, two unique species as to the evolution of this enzyme family. We identify chimeric RNAs from the human AOX3 and AOX3L1 pseudogenes with potential to encode a novel microRNA.
Collapse
Affiliation(s)
- Mami Kurosaki
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche “Mario Negri”, via La Masa 19, 20156 Milan, Italy
| | - Marco Bolis
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche “Mario Negri”, via La Masa 19, 20156 Milan, Italy
| | - Maddalena Fratelli
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche “Mario Negri”, via La Masa 19, 20156 Milan, Italy
| | - Maria Monica Barzago
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche “Mario Negri”, via La Masa 19, 20156 Milan, Italy
| | - Linda Pattini
- Department of Bioengineering, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Gemma Perretta
- Istututo di Biologia Cellulare e Neurobiologia, Consiglio Nazionale delle Ricerche, via Anguillarese 301, 00123 Rome, Italy
| | - Mineko Terao
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche “Mario Negri”, via La Masa 19, 20156 Milan, Italy
| | - Enrico Garattini
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche “Mario Negri”, via La Masa 19, 20156 Milan, Italy
| |
Collapse
|
42
|
Garattini E, Fisher JN, Paroni G, Centritto F, Goodall GJ, Tsykin A, Fratelli M, Terao M. Abstract 3088: Combinations of lapatinib and all-trans retinoic acid control the coordinate expression of microRNA modules and target-mRNAs in ERBB2+/RARA+ breast carcinoma cells: Significance for the antitumor activity. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-3088] [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
In a recent report (Paroni et al, Oncogene, 31:3431-43, 2012), we demonstrated that 25% of all ERBB2+ breast cancers present with a co-amplification of the RARA locus, encoding the nuclear retinoic acid receptor, RARα. ERBB2+/RARA+ breast cancer cell lines, like SKBR3 and AU565, are sensitive to the anti-proliferative and cyto-differentiating effects of all-trans retinoic acid (ATRA), whereas the ERBB2+/RARA− counterparts are refractory. Simultaneous targeting of RARα with ATRA and ERBB2 with lapatinib in SKBR3 and AU565 cells leads to synergistic interactions as to growth inhibition and cyto-differentiation. In addition, combinations of ATRA and lapatinib exert an apoptotic effect, which is not observed with the single components. This suggests that ERBB2+/RARA+ breast cancer patients may benefit from lapatinib+ATRA regimens and represent the rationale of an ongoing clinical trial.
The use of lapatinib and ATRA for the stratified therapy of ERBB2+/RARA+ patients requires knowledge of the molecular mechanisms underlying the cross-talk between the two compounds. We evaluated the effects of lapatinib and/or ATRA on the expression profiles of more than 1,000 microRNAs in SKBR3 cells using an appropriate microarray platform. Both lapatinib and ATRA caused up- and down-regulation of numerous microRNAs. The combination of the two compounds enhanced the action of the single components of the mixture and resulted in the up- and down-regulation of novel target microRNAs as well. We integrated these results with microRNA-target-gene prediction algorithms and whole-genome gene-expression data looking for significant correlations between microRNA and potential/established target mRNA levels. Network analysis led to the identification of two highly interconnected microRNA/target-mRNA modules controlled in opposite directions by lapatinib+ATRA. The first one consists of six microRNAs (miR-1207-5-p, miR-874, miR-134, miR-762, miR-1181 and miR-320c) which are up-regulated by lapatinib+ATRA and control a common set of down-regulated target mRNAs in a coordinate fashion. Most of the mRNAs of the module control cell proliferation in a positive fashion. The second network consists of seven microRNAs (miR-203, miR-125a-5p, miR-193a-5p, miR-210, miR-362-5p, miR-532-5p and miR-342-3p) which are down-regulated by lapatinib+ATRA and control a series of up-regulated target-mRNAs. In this case, the majority of regulated genes is involved in negative regulation of cell proliferation. Coordinated regulation of microRNA sets controlling a common group of genes and functions represents a new concept that deserves further studies. Currently, we are in the process of establishing the functional significance of the identified microRNA modules for the anti-tumor effects of lapatinib and ATRA.
Citation Format: Enrico Garattini, James N. Fisher, Gabriela Paroni, Floriana Centritto, Gregory J. Goodall, Anna Tsykin, Maddalena Fratelli, Mineko Terao. Combinations of lapatinib and all-trans retinoic acid control the coordinate expression of microRNA modules and target-mRNAs in ERBB2+/RARA+ breast carcinoma cells: Significance for the antitumor activity. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3088. doi:10.1158/1538-7445.AM2013-3088
Collapse
Affiliation(s)
| | | | | | | | - Gregory J. Goodall
- 2Centre for Cancer Biology, SA Pathology, Adelaide, Australia and Department of Medicine, University of Adelaide, Adelaide, Australia
| | - Anna Tsykin
- 2Centre for Cancer Biology, SA Pathology, Adelaide, Australia and Department of Medicine, University of Adelaide, Adelaide, Australia
| | | | - Mineko Terao
- 1Istituto di Ricerche Farmacologiche, Milano, Italy
| |
Collapse
|
43
|
Paroni G, Fratelli M, Flora M, Zanetti A, Centritto F, Affatato R, Ubezio P, Terao M, Gardini G, Garattini E. 1057 Synergistic Antitumor Activity of Lapatinib and Retinoids on a Novel Subtype of Breast Cancer With Co-amplification of ERBB2 and RARA. Eur J Cancer 2012. [DOI: 10.1016/s0959-8049(12)71668-4] [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: 11/30/2022]
|
44
|
Locatelli D, Terao M, Fratelli M, Zanetti A, Kurosaki M, Lupi M, Barzago MM, Uggetti A, Capra S, D'Errico P, Battaglia GS, Garattini E. Human axonal survival of motor neuron (a-SMN) protein stimulates axon growth, cell motility, C-C motif ligand 2 (CCL2), and insulin-like growth factor-1 (IGF1) production. J Biol Chem 2012; 287:25782-94. [PMID: 22669976 PMCID: PMC3406665 DOI: 10.1074/jbc.m112.362830] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [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] [Indexed: 11/06/2022] Open
Abstract
Spinal muscular atrophy is a fatal genetic disease of motoneurons due to loss of full-length survival of motor neuron protein, the main product of the disease gene SMN1. Axonal SMN (a-SMN) is an alternatively spliced isoform of SMN1, generated by retention of intron 3. To study a-SMN function, we generated cellular clones for the expression of the protein in mouse motoneuron-like NSC34 cells. The model was instrumental in providing evidence that a-SMN decreases cell growth and plays an important role in the processes of axon growth and cellular motility. In our conditions, low levels of a-SMN expression were sufficient to trigger the observed biological effects, which were not modified by further increasing the amounts of the expressed protein. Differential transcriptome analysis led to the identification of novel a-SMN-regulated factors, i.e. the transcripts coding for the two chemokines, C-C motif ligands 2 and 7 (CCL2 and CCL7), as well as the neuronal and myotrophic factor, insulin-like growth factor-1 (IGF1). a-SMN-dependent induction of CCL2 and IGF1 mRNAs resulted in increased intracellular levels and secretion of the respective protein products. Induction of CCL2 contributes to the a-SMN effects, mediating part of the action on axon growth and random cell motility, as indicated by chemokine knockdown and re-addition studies. Our results shed new light on a-SMN function and the underlying molecular mechanisms. The data provide a rational framework to understand the role of a-SMN deficiency in the etiopathogenesis of spinal muscular atrophy.
Collapse
Affiliation(s)
- Denise Locatelli
- Molecular Neuroanatomy Laboratory, Department of Experimental Neurophysiology and Epileptology, Istituto Neurologico "C. Besta," via Celoria 11, 20133 Milano, Italy
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Terao M, Fratelli M, Kurosaki M, Zanetti A, Guarnaccia V, Paroni G, Tsykin A, Lupi M, Gianni M, Goodall GJ, Garattini E. Induction of miR-21 by retinoic acid in estrogen receptor-positive breast carcinoma cells: biological correlates and molecular targets. J Biol Chem 2010; 286:4027-42. [PMID: 21131358 DOI: 10.1074/jbc.m110.184994] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Retinoids are promising agents for the treatment/prevention of breast carcinoma. We examined the role of microRNAs in mediating the effects of all-trans-retinoic acid (ATRA), which suppresses the proliferation of estrogen receptor-positive (ERα(+)) breast carcinoma cells, such as MCF-7, but not estrogen receptor-negative cells, such as MDA-MB-231. We found that pro-oncogenic miR-21 is selectively induced by ATRA in ERα(+) cells. Induction of miR-21 counteracts the anti-proliferative action of ATRA but has the potentially beneficial effect of reducing cell motility. In ERα(+) cells, retinoid-dependent induction of miR-21 is due to increased transcription of the MIR21 gene via ligand-dependent activation of the nuclear retinoid receptor, RARα. RARα is part of the transcription complex present in the 5'-flanking region of the MIR21 gene. The receptor binds to two functional retinoic acid-responsive elements mapping upstream of the transcription initiation site. Silencing of miR-21 enhances ATRA-dependent growth inhibition and senescence while reverting suppression of cell motility afforded by the retinoid. Up-regulation of miR-21 results in retinoid-dependent inhibition of the established target, maspin. Knockdown and overexpression of maspin in MCF-7 cells indicates that the protein is involved in ATRA-induced growth inhibition and contributes to the ATRA-dependent anti-motility responses. Integration between whole genome analysis of genes differentially regulated by ATRA in MCF-7 and MDA-MB-231 cells, prediction of miR-21 regulated genes, and functional studies led to the identification of three novel direct miR-21 targets: the pro-inflammatory cytokine IL1B, the adhesion molecule ICAM-1 and PLAT, the tissue-type plasminogen activator. Evidence for ICAM-1 involvement in retinoid-dependent inhibition of MCF-7 cell motility is provided.
Collapse
Affiliation(s)
- Mineko Terao
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri, 20156 Milano, Italy
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Binaschi M, Boldetti A, Gianni M, Maggi CA, Gensini M, Bigioni M, Parlani M, Giolitti A, Fratelli M, Valli C, Terao M, Garattini E. Antiproliferative and differentiating activities of a novel series of histone deacetylase inhibitors. ACS Med Chem Lett 2010; 1:411-5. [PMID: 24900225 DOI: 10.1021/ml1001163] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [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: 05/18/2010] [Accepted: 06/30/2010] [Indexed: 11/28/2022] Open
Abstract
Histone deacetylases are promising molecular targets for the development of antitumor agents. A novel series of histone deacetylase inhibitors of the hydroxamic acid type were synthesized for structure-activity studies. Thirteen tricyclic dibenzo-diazepine, -oxazepine, and -thiazepine analogues were studied and shown to induce variable degrees of histone H3/H4 and tubulin acetylation in a cellular model of myeloid leukemia sensitive to all-trans retinoic acid (ATRA). Multiparametric correlations between acetylation of the three substrates, tumor cell growth inhibition, and ATRA-dependent cytodifferentiation were performed, providing information on the chemical functionalities governing these activities. For two analogues, antitumor activity in the animal was demonstrated.
Collapse
Affiliation(s)
- Monica Binaschi
- Menarini Ricerche S.p.A., Via Tito Speri 10, 00040 Pomezia (Roma), Italy
| | - Andrea Boldetti
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche “Mario Negri”, via La Masa 19, 20156 Milano, Italy
| | - Maurizio Gianni
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche “Mario Negri”, via La Masa 19, 20156 Milano, Italy
| | | | - Martina Gensini
- Menarini Ricerche S.p.A., Via Tito Speri 10, 00040 Pomezia (Roma), Italy
| | - Mario Bigioni
- Menarini Ricerche S.p.A., Via Tito Speri 10, 00040 Pomezia (Roma), Italy
| | - Massimo Parlani
- Menarini Ricerche S.p.A., Via Tito Speri 10, 00040 Pomezia (Roma), Italy
| | | | - Maddalena Fratelli
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche “Mario Negri”, via La Masa 19, 20156 Milano, Italy
| | - Claudia Valli
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche “Mario Negri”, via La Masa 19, 20156 Milano, Italy
| | - Mineko Terao
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche “Mario Negri”, via La Masa 19, 20156 Milano, Italy
| | - Enrico Garattini
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche “Mario Negri”, via La Masa 19, 20156 Milano, Italy
| |
Collapse
|
47
|
Abstract
Aldehyde oxidases (EC 1.2.3.1) are a small group of structurally conserved cytosolic proteins represented in both the animal and plant kingdoms. In vertebrates, aldehyde oxidases constitute the small sub-family of molybdo-flavoenzymes, along with the evolutionarily and structurally related protein, xanthine oxidoreductase. These enzymes require a molybdo-pterin cofactor (molybdenum cofactor, MoCo) and flavin adenine dinucleotide for their catalytic activity. Aldehyde oxidases have broad substrate specificity and catalyse the hydroxylation of N-heterocycles and the oxidation of aldehydes to the corresponding acid. In humans, a single aldehyde oxidase gene (AOX1) and two pseudogenes clustering on a short stretch of chromosome 2q are known. In other mammals, a variable number of structurally conserved aldehyde oxidase genes has been described. Four genes (Aox1, Aox3, Aox4 and Aox3l1), coding for an equivalent number of catalytically active enzymes, are present in the mouse and rat genomes. Although human AOX1 and its homologous proteins are best known as drug metabolising enzymes, the physiological substrate(s) and function(s) are as yet unknown. The present paper provides an update of the available information on the evolutionary history, tissue- and cell-specific distribution and function of mammalian aldehyde oxidases.
Collapse
Affiliation(s)
- Enrico Garattini
- Laboratory of Molecular Biology, Department of Biochemistry and Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri, via La Masa 19, 20156 Milano, Italy.
| | | | | |
Collapse
|
48
|
Valli C, Paroni G, Di Francesco AM, Riccardi R, Tavecchio M, Erba E, Boldetti A, Gianni' M, Fratelli M, Pisano C, Merlini L, Antoccia A, Cenciarelli C, Terao M, Garattini E. Atypical retinoids ST1926 and CD437 are S-phase-specific agents causing DNA double-strand breaks: significance for the cytotoxic and antiproliferative activity. Mol Cancer Ther 2008; 7:2941-54. [DOI: 10.1158/1535-7163.mct-08-0419] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
49
|
Parrella E, Giannì M, Fratelli M, Barzago MM, Raska I, Diomede L, Kurosaki M, Pisano C, Carminati P, Merlini L, Dallavalle S, Tavecchio M, Rochette-Egly C, Terao M, Garattini E. Antitumor activity of the retinoid-related molecules (E)-3-(4'-hydroxy-3'-adamantylbiphenyl-4-yl)acrylic acid (ST1926) and 6-[3-(1-adamantyl)-4-hydroxyphenyl]-2-naphthalene carboxylic acid (CD437) in F9 teratocarcinoma: Role of retinoic acid receptor gamma and retinoid-independent pathways. Mol Pharmacol 2006; 70:909-24. [PMID: 16788091 DOI: 10.1124/mol.106.023614] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [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: 11/22/2022] Open
Abstract
The retinoid-related molecules (RRMs) ST1926 [(E)-3-(4'-hydroxy-3'-adamantylbiphenyl-4-yl)acrylic acid] and CD437 (6-[3-(1-adamantyl)-4-hydroxyphenyl]-2-naphthalene carboxylic acid) are promising anticancer agents. We compared the retinoic acid receptor (RAR) trans-activating properties of the two RRMs and all-trans-retinoic acid (ATRA). ST1926 and CD437 are better RARgamma agonists than ATRA. We used three teratocarcinoma cell lines to evaluate the significance of RARgamma in the activity of RRMs: F9-wild type (WT); F9gamma-/-, lacking the RARgamma gene; F9gamma51, aF9gamma-/-derivative, complemented for the RARgamma deficit. Similar to ATRA, ST1926 and CD437 activate cytodifferentiation only in F9-WT cells. Unlike ATRA, ST1926 and CD437 arrest cells in the G2/M phase of the cell cycle and induce apoptosis in all F9 cell lines. Our data indicate that RARgamma and the classic retinoid pathway are not relevant for the antiproliferative and apoptotic activities of RRMs in vitro. Increases in cytosolic calcium are fundamental for apoptosis, in that intracellular calcium chelators abrogate the process. Comparison of the gene expression profiles associated with ST1926 and ATRA in F9-WT and F9gamma-/-indicates that the RRM activates a conspicuous nonretinoid response in addition to the classic and RAR-dependent pathway. The pattern of genes regulated by ST1926 selectively, in a RARgamma-independent manner, provides novel insights into the possible molecular determinants underlying the activity of RRMs in vitro. Furthermore, it suggests that RARgamma-dependent responses are relevant to the activity of RRMs in vivo. Indeed, the receptor hinders the antitumor activity in vivo, in that both syngeneic and immunosuppressed SCID mice bearing F9gamma-/- tumors have increased life spans after treatment with ST1926 and CD437 relative to their F9-WT counterparts.
Collapse
|
50
|
Abstract
Aldehyde oxidases are molybdo-flavoenzymes structurally related to xanthine oxidoreductase. They catalyze the oxidation of aldehydes or N-heterocycles of physiological, pharmacological, and toxicological relevance. Rodents are characterized by four aldehyde oxidases as follows: AOX1 and aldehyde oxidase homologs 1-3 (AOH1, AOH2, and AOH3). Humans synthesize a single functional aldehyde oxidase, AOX1. Here we define the structure and the characteristics of the aldehyde oxidase genes and proteins in chicken and dog. The avian genome contains two aldehyde oxidase genes, AOX1 and AOH, mapping to chromosome 7. AOX1 and AOH are structurally very similar and code for proteins whose sequence was deduced from the corresponding cDNAs. AOX1 is the ortholog of the same gene in mammals, whereas AOH represents the likely ancestor of rodent AOH1, AOH2, and AOH3. The dog genome is endowed with two structurally conserved and active aldehyde oxidases clustering on chromosome 37. Cloning of the corresponding cDNAs and tissue distribution studies demonstrate that they are the orthologs of rodent AOH2 and AOH3. The vestiges of dog AOX1 and AOH1 are recognizable upstream of AOH2 and AOH3 on the same chromosome. Comparison of the complement and the structure of the aldehyde oxidase and xanthine oxidoreductase genes in vertebrates and other animal species indicates that they evolved through a series of duplication and inactivation events. Purification of the chicken AOX1 protein to homogeneity from kidney demonstrates that the enzyme possesses retinaldehyde oxidase activity. Unlike humans and most other mammals, dog and chicken are devoid of liver aldehyde oxidase activity.
Collapse
Affiliation(s)
- Mineko Terao
- Laboratory of Molecular Biology, Centro Catullo e Daniela Borgomainerio, Istituto di Ricerche Farmacologiche Mario Negri, via Eritrea 62, 20157 Milano, Italy
| | | | | | | | | | | | | | | |
Collapse
|