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Bendixen KK, Forsberg-Pho S, Dazio G, Hansen EE, Eriksen SK, Epistolio S, Merlo E, Boldorini R, Venesio T, Movilia A, Caprera C, Arnspang EC, Børgesen M, Christensen UB, Frattini M, Petersen RK. One-instrument, objective microsatellite instability analysis using high-resolution melt. PLoS One 2024; 19:e0302274. [PMID: 38662796 PMCID: PMC11045061 DOI: 10.1371/journal.pone.0302274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
Abstract
In recent years, immune checkpoint inhibitors have proved immense clinical progression in the treatment of certain cancers. The efficacy of immune checkpoint inhibitors is correlated with mismatch repair system deficiency and is exceptionally administered based exclusively on this biological mechanism independent of the cancer type. The promising effect of immune checkpoint inhibitors has left an increasing demand for analytical tools evaluating the mismatch repair status. The analysis of microsatellite instability (MSI), reflecting an indirect but objective manner the inactivation of the mismatch repair system, plays several roles in clinical practice and, therefore, its evaluation is of high relevance. Analysis of MSI by PCR followed by fragment analysis on capillary electrophoresis remains the gold standard method for detection of a deficient mismatch repair system and thereby treatment with immune checkpoint inhibitors. Novel technologies have been applied and concepts such as tumor mutation burden have been introduced. However, to date, most of these technologies require high costs or the need of matched non-tumor tissue as internal comparator. In this study, we present a novel, one-instrument, fast, and objective method for the detection of MSI (MicroSight® MSI 1-step HRM Analysis), which does not depend on the use of matched non-tumor tissue. The assay analyzes five well-described mononucleotide microsatellite sequences by real-time PCR followed by high-resolution melt and evaluates microsatellite length variations via PCR product melting profiles. The assay was evaluated using two different patient cohorts and evaluation included several DNA extraction methodologies, two different PCR platforms, and an inter-laboratory ring study. The MicroSight® MSI assay showed a high repeatability regardless of DNA extraction method and PCR platform, and a 100% agreement of the MSI status with PCR fragment analysis methods applied as clinical comparator.
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Affiliation(s)
| | | | - Giulia Dazio
- Institute of Pathology, Ente Ospedaliero Cantonale, Locarno, Switzerland
| | | | | | - Samantha Epistolio
- Institute of Pathology, Ente Ospedaliero Cantonale, Locarno, Switzerland
| | - Elisabetta Merlo
- Institute of Pathology, Ente Ospedaliero Cantonale, Locarno, Switzerland
| | - Renzo Boldorini
- Unit of Pathology, Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Tiziana Venesio
- Candiolo Cancer Institute, Fondazione del Piemonte per l’Oncologia, Candiolo, Italy
| | - Alessandra Movilia
- Hospital of Legnano, SS Biologia Molecolare, UO Anatomia Patologica, Azienda Socio Sanitaria Territoriale Ovest Milanese, Ospedale di Legnano, Legnano, Italy
| | - Cecilia Caprera
- Laboratory of Molecular Oncology and Predictive Medicine, Pathology Unit, Azienda Ospedaliera Santa Maria di Terni, Terni, Italy
| | - Eva Christensen Arnspang
- Department of Green Technology, Faculty of Engineering, University of Southern Denmark, Odense, Denmark
| | | | | | - Milo Frattini
- Institute of Pathology, Ente Ospedaliero Cantonale, Locarno, Switzerland
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Pepe F, Russo G, Venuta A, Scimone C, Nacchio M, Pisapia P, Goteri G, Barbisan F, Chiappetta C, Pernazza A, Campagna D, Giordano M, Perrone G, Sabarese G, Altimari A, de Biase D, Tallini G, Calistri D, Chiadini E, Capelli L, Santinelli A, Gulini AE, Pierpaoli E, Badiali M, Murru S, Murgia R, Guerini Rocco E, Venetis K, Fusco N, Morotti D, Gianatti A, Furlan D, Rossi G, Melocchi L, Russo M, De Luca C, Palumbo L, Simonelli S, Maffè A, Francia di Celle P, Venesio T, Scatolini M, Grosso E, Orecchia S, Fassan M, Balistreri M, Zulato E, Reghellin D, Lazzari E, Santacatterina M, Piredda ML, Riccardi M, Laurino L, Roz E, Longo D, Romeo DP, Fazzari C, Moreno-Manuel A, Puglia GD, Prjibelski AD, Shafranskaya D, Righi L, Listì A, Vitale D, Iaccarino A, Malapelle U, Troncone G. Non-Small Cell Lung Cancer Testing on Reference Specimens: An Italian Multicenter Experience. Oncol Ther 2024; 12:73-95. [PMID: 38200361 PMCID: PMC10881930 DOI: 10.1007/s40487-023-00252-5] [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: 09/08/2023] [Accepted: 11/02/2023] [Indexed: 01/12/2024] Open
Abstract
INTRODUCTION Biomarker testing is mandatory for the clinical management of patients with advanced non-small cell lung cancer (NSCLC). Myriads of technical platforms are now available for biomarker analysis with differences in terms of multiplexing capability, analytical sensitivity, and turnaround time (TAT). We evaluated the technical performance of the diagnostic workflows of 24 representative Italian institutions performing molecular tests on a series of artificial reference specimens built to mimic routine diagnostic samples. METHODS Sample sets of eight slides from cell blocks of artificial reference specimens harboring exon 19 EGFR (epidermal growth factor receptor) p.E746_AT50del, exon 2 KRAS (Kirsten rat sarcoma viral oncogene homologue) p.G12C, ROS1 (c-ros oncogene 1)-unknown gene fusion, and MET (MET proto-oncogene, receptor tyrosine kinase) Δ exon 14 skipping were distributed to each participating institution. Two independent cell block specimens were validated by the University of Naples Federico II before shipment. Methodological and molecular data from reference specimens were annotated. RESULTS Overall, a median DNA concentration of 3.3 ng/µL (range 0.1-10.0 ng/µL) and 13.4 ng/µL (range 2.0-45.8 ng/µL) were obtained with automated and manual technical procedures, respectively. RNA concentrations of 5.7 ng/µL (range 0.2-11.9 ng/µL) and 9.3 ng/µL (range 0.5-18.0 ng/µL) were also detected. KRAS exon 2 p.G12C, EGFR exon 19 p.E736_A750del hotspot mutations, and ROS1 aberrant transcripts were identified in all tested cases, whereas 15 out of 16 (93.7%) centers detected MET exon 14 skipping mutation. CONCLUSIONS Optimized technical workflows are crucial in the decision-making strategy of patients with NSCLC. Artificial reference specimens enable optimization of diagnostic workflows for predictive molecular analysis in routine clinical practice.
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Affiliation(s)
- Francesco Pepe
- Department of Public Health, Federico II University of Naples, Via S. Pansini, 5, 80131, Naples, Italy
| | - Gianluca Russo
- Department of Public Health, Federico II University of Naples, Via S. Pansini, 5, 80131, Naples, Italy
| | - Alessandro Venuta
- Department of Public Health, Federico II University of Naples, Via S. Pansini, 5, 80131, Naples, Italy
| | - Claudia Scimone
- Department of Public Health, Federico II University of Naples, Via S. Pansini, 5, 80131, Naples, Italy
| | - Mariantonia Nacchio
- Department of Public Health, Federico II University of Naples, Via S. Pansini, 5, 80131, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, Federico II University of Naples, Via S. Pansini, 5, 80131, Naples, Italy
| | - Gaia Goteri
- Pathological Anatomy Institute, Polytechnic University of Marche Region, Ancona, Italy
| | - Francesca Barbisan
- Pathological Anatomy Institute, Polytechnic University of Marche Region, Ancona, Italy
| | | | - Angelina Pernazza
- Department of Medico-Surgical Sciences and Biotechnologies, Polo Pontino-Sapienza University, Latina, Italy
| | - Domenico Campagna
- Department of Pathology, San Giovanni-Addolorata Hospital, 00184, Rome, Italy
| | - Marco Giordano
- Department of Pathology, San Giovanni-Addolorata Hospital, 00184, Rome, Italy
| | - Giuseppe Perrone
- Research Unit of Anatomical Pathology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21-00128, Rome, Italy
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200-00128, Rome, Italy
| | - Giovanna Sabarese
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200-00128, Rome, Italy
| | - Annalisa Altimari
- Molecular Pathology, University of Bologna Hospital of Bologna Sant'Orsola-Malpighi Polyclinic, Bologna, Italy
| | - Dario de Biase
- Pharmacy and Biotechnology (FaBiT), Molecular Pathology Laboratory, University of Bologna, Bologna, Italy
| | - Giovanni Tallini
- Molecular Pathology, University of Bologna Hospital of Bologna Sant'Orsola-Malpighi Polyclinic, Bologna, Italy
- Pharmacy and Biotechnology (FaBiT), Molecular Pathology Laboratory, University of Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Daniele Calistri
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014, Meldola, Italy
| | - Elisa Chiadini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014, Meldola, Italy
| | - Laura Capelli
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014, Meldola, Italy
| | - Alfredo Santinelli
- Anatomic Pathology Azienda Sanitaria Territoriale Pesaro-Urbino, Pesaro, Italy
| | - Anna Elisa Gulini
- Anatomic Pathology Azienda Sanitaria Territoriale Pesaro-Urbino, Pesaro, Italy
| | - Elisa Pierpaoli
- Anatomic Pathology Azienda Sanitaria Territoriale Pesaro-Urbino, Pesaro, Italy
| | - Manuela Badiali
- Laboratory of Genetics and Genomics-Pediatric Hospital A.Cao-ASL8, Cagliari, Italy
| | - Stefania Murru
- Laboratory of Genetics and Genomics-Pediatric Hospital A.Cao-ASL8, Cagliari, Italy
| | - Riccardo Murgia
- Experimental Medicine Unit, Department of Biomedical Sciences, University of Cagliari, 09124, Cagliari, Italy
| | - Elena Guerini Rocco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono 7, 20122, Milan, Italy
| | - Konstantinos Venetis
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono 7, 20122, Milan, Italy
| | - Denise Morotti
- Pathology Unit and Medical Genetics Laboratory, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Andrea Gianatti
- Pathology Unit and Medical Genetics Laboratory, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Daniela Furlan
- Pathology Unit, Department of Medicine and Technological Innovation, University of Insubria, Varese, Italy
| | - Giulio Rossi
- Department of Anatomical Pathology, Fondazione Poliambulanza, 25124, Brescia, Italy
| | - Laura Melocchi
- Department of Anatomical Pathology, Fondazione Poliambulanza, 25124, Brescia, Italy
| | - Maria Russo
- Department of Public Health, Federico II University of Naples, Via S. Pansini, 5, 80131, Naples, Italy
| | - Caterina De Luca
- Department of Public Health, Federico II University of Naples, Via S. Pansini, 5, 80131, Naples, Italy
| | - Lucia Palumbo
- Department of Public Health, Federico II University of Naples, Via S. Pansini, 5, 80131, Naples, Italy
| | - Saverio Simonelli
- Department of Public Health, Federico II University of Naples, Via S. Pansini, 5, 80131, Naples, Italy
| | - Antonella Maffè
- Genetics and Molecular Biology Unit, Santa Croce e Carle Hospital, 12100, Cuneo, Italy
| | - Paola Francia di Celle
- Molecular Pathology, AOU Città della Salute e della Scienza di Torino, 10126, Turin, Italy
| | - Tiziana Venesio
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, Italy
| | - Maria Scatolini
- Molecular Oncology Lab, Fondazione Edo ed Elvo Tempia, Biella, Italy
| | - Enrico Grosso
- Molecular Oncology Lab, Fondazione Edo ed Elvo Tempia, Biella, Italy
| | - Sara Orecchia
- Pathology Division, S. Antonio and Biagio Hospital, Alessandria, Italy
| | - Matteo Fassan
- Department of Medicine-DIMED, University of Padua, Padua, Veneto, Italy
- Veneto Institute of Oncology-IOV-IRCCS, Padua, Italy
| | | | | | | | - Elena Lazzari
- Department of Pathology, San Bortolo Hospital, Vicenza, Italy
| | | | | | - Manuela Riccardi
- Department of Pathology, Azienda Ulss3 Serenissima, Ospedale dell'Angelo, Venice, Italy
| | - Licia Laurino
- Department of Pathology, Azienda Ulss3 Serenissima, Ospedale dell'Angelo, Venice, Italy
| | - Elena Roz
- Pathology Unit, La Maddalena Clinic for Cancer, Palermo, Italy
| | - Domenico Longo
- UOSD di Anatomia Patologica dell'Azienda Ospedaliera Papardo, Messina, Italy
| | | | - Carmine Fazzari
- UOSD di Anatomia Patologica dell'Azienda Ospedaliera Papardo, Messina, Italy
| | - Andrea Moreno-Manuel
- Molecular Oncology Laboratory, Fundación Investigación Hospital General Universitario de Valencia, 46014, Valencia, Spain
- TRIAL Mixed Unit, Centro Investigación Príncipe Felipe-Fundación Investigación Hospital General Universitario de Valencia, 46014, Valencia, Spain
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, 28029, Madrid, Spain
| | - Giuseppe Diego Puglia
- Institute for Agricultural and Forest Systems in the Mediterranean, National Research Council (ISAFOM-CNR), 95128, Catania, Italy
| | - Andrey D Prjibelski
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Daria Shafranskaya
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Luisella Righi
- Department of Oncology, San Luigi Hospital, University of Turin, Orbassano, TO, Italy
| | - Angela Listì
- Department of Oncology, San Luigi Hospital, University of Turin, Orbassano, TO, Italy
| | - Domenico Vitale
- Department of Public Health, Federico II University of Naples, Via S. Pansini, 5, 80131, Naples, Italy
| | - Antonino Iaccarino
- Department of Public Health, Federico II University of Naples, Via S. Pansini, 5, 80131, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, Federico II University of Naples, Via S. Pansini, 5, 80131, Naples, Italy.
| | - Giancarlo Troncone
- Department of Public Health, Federico II University of Naples, Via S. Pansini, 5, 80131, Naples, Italy
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3
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Pallocca M, Molineris I, Berrino E, Marcozzi B, Betti M, Levati L, D'Atri S, Menin C, Madonna G, Ghiorzo P, Bulgarelli J, Ferraresi V, Venesio T, Rodolfo M, Rivoltini L, Lanfrancone L, Ascierto PA, Mazzarella L, Pelicci PG, De Maria R, Ciliberto G, Medico E, Russo G. Comprehensive genomic profiling on metastatic Melanoma: results from a network screening from 7 Italian Cancer Centres. J Transl Med 2024; 22:29. [PMID: 38184610 PMCID: PMC10770968 DOI: 10.1186/s12967-023-04776-2] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/28/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND The current therapeutic algorithm for Advanced Stage Melanoma comprises of alternating lines of Targeted and Immuno-therapy, mostly via Immune-Checkpoint blockade. While Comprehensive Genomic Profiling of solid tumours has been approved as a companion diagnostic, still no approved predictive biomarkers are available for Melanoma aside from BRAF mutations and the controversial Tumor Mutational Burden. This study presents the results of a Multi-Centre Observational Clinical Trial of Comprehensive Genomic Profiling on Target and Immuno-therapy treated advanced Melanoma. METHODS 82 samples, collected from 7 Italian Cancer Centres of FFPE-archived Metastatic Melanoma and matched blood were sequenced via a custom-made 184-gene amplicon-based NGS panel. Sequencing and bioinformatics analysis was performed at a central hub. Primary analysis was carried out via the Ion Reporter framework. Secondary analysis and Machine Learning modelling comprising of uni and multivariate, COX/Lasso combination, and Random Forest, was implemented via custom R/Python scripting. RESULTS The genomics landscape of the ACC-mela cohort is comparable at the somatic level for Single Nucleotide Variants and INDELs aside a few gene targets. All the clinically relevant targets such as BRAF and NRAS have a comparable distribution thus suggesting the value of larger scale sequencing in melanoma. No comparability is reached at the CNV level due to biotechnological biases and cohort numerosity. Tumour Mutational Burden is slightly higher in median for Complete Responders but fails to achieve statistical significance in Kaplan-Meier survival analysis via several thresholding strategies. Mutations on PDGFRB, NOTCH3 and RET were shown to have a positive effect on Immune-checkpoint treatment Overall and Disease-Free Survival, while variants in NOTCH4 were found to be detrimental for both endpoints. CONCLUSIONS The results presented in this study show the value and the challenge of a genomics-driven network trial. The data can be also a valuable resource as a validation cohort for Immunotherapy and Target therapy genomic biomarker research.
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Affiliation(s)
- Matteo Pallocca
- Biostatistics, Bioinformatics and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
| | - Ivan Molineris
- Department of Life Science and System Biology, University of Turin, Via Accademia Albertina 13, 10123, Turin, Italy
- University of Turin at Candiolo Cancer Institute, Turin, Italy
| | - Enrico Berrino
- University of Turin at Candiolo Cancer Institute, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Benedetta Marcozzi
- Biostatistics, Bioinformatics and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Martina Betti
- Biostatistics, Bioinformatics and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | | | | | - Chiara Menin
- Immunology and Oncological Molecular Diagnostics, Oncological Institute, IOV IRCCS UOC, Padua, Italy
| | - Gabriele Madonna
- Melanoma, Cancer Immunotherapy and Development Therapeutics, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, 80131, Naples, Italy
| | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
- Department of Internal Medicine and Medical Specialties, University of Genova, 16132, Genoa, Italy
| | - Jenny Bulgarelli
- Immunotherapy, Cell Therapy and Biobank Unit, IRCCS Istituto Romagnolo Per lo Studio dei Tumori (IRST) "Dino Amadori", 47014, Meldola, Italy
| | - Virgina Ferraresi
- Sarcoma and Rare Tumours Departmental Unit- IRCCS Regina Elena National Cancer Institute-Rome, Rome, Italy
| | - Tiziana Venesio
- University of Turin at Candiolo Cancer Institute, Turin, Italy
| | - Monica Rodolfo
- Unit of Translational Immunology, Department of Experimental Oncology, IRCCS Foundation National Cancer Institute, Milan, Italy
| | - Licia Rivoltini
- Unit of Translational Immunology, Department of Experimental Oncology, IRCCS Foundation National Cancer Institute, Milan, Italy
| | - Luisa Lanfrancone
- Department of Experimental Oncology, European Institute of Oncology IRCCS (IEO), Milan, Italy
| | - Paolo Antonio Ascierto
- Immunology and Oncological Molecular Diagnostics, Oncological Institute, IOV IRCCS UOC, Padua, Italy
| | - Luca Mazzarella
- Institute of General Pathology, Catholic University "Sacro Cuore", Rome, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology IRCCS (IEO), Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Ruggero De Maria
- Institute of General Pathology, Catholic University "Sacro Cuore", Rome, Italy
| | - Gennaro Ciliberto
- Scientific Direction, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Enzo Medico
- University of Turin at Candiolo Cancer Institute, Turin, Italy
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Rizzo A, Cantale O, Mogavero A, Garetto L, Racca M, Venesio T, Anpalakhan S, Novello S, Gregorc V, Banna GL. Assessing the role of colonic and other anatomical sites uptake by [ 18 F]FDG-PET/CT and immune-inflammatory peripheral blood indexes in patients with advanced non-small cell lung cancer treated with first-line immune checkpoint inhibitors. Thorac Cancer 2023; 14:2473-2483. [PMID: 37442801 PMCID: PMC10447168 DOI: 10.1111/1759-7714.15032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Inflammation in non-small cell lung cancer (NSCLC) may impair the response to immune checkpoint inhibitors (ICIs) and can be indicated by peripheral blood inflammatory indexes. 2-deoxy-2-[18 F]fluoro-D-glucose positron emission tomography/computed tomography ([18 F] FDG-PET/CT) may be used as a marker of inflammation by measuring glucose metabolism in different colonic sites. METHODS This retrospective analysis aimed to investigate the correlation between [18 F] FDGPET/CT SUVratio in six gastrointestinal districts, the spleen, the pharynx and the larynx alongside the most avid tumor lesion with peripheral blood inflammatory indexes, including the neutrophil-to-lymphocyte ratio (NLR), systemic immune-inflammatory index (SII, i.e., NLR times platelets) and lactate dehydrogenase (LDH), in patients with [18 F] FDG-PET/CT staged IV NSCLC who received first-line immune checkpoint inhibitors (ICIs). The role of SUVratios and peripheral blood inflammatory indexes in predicting overall survival (OS) and progression-free survival (PFS) was then explored. RESULTS A total of 43 patients were treated with first-line ICI alone (58%) or in combination with chemotherapy (42%). A significant correlation was only found between the rectosigmoid SUVratio and NLR (p = 0.0465). NLR >5.5 and LDH > 333.5 were associated with a worse OS (p = 0.033 and p = 0.009, respectively). The SII was associated with a worse PFS in patients treated with ICI alone (p = 0.033). None of the SUVratios were significantly associated with OS or PFS, although a high left colon SUVratio showed a trend toward a worse PFS. CONCLUSION There was no significant correlation between [18 F]FDG PET/CT uptake in different anatomical sites, and in the tumor, and systemic immune-inflammatory indexes. The prognostic role of high left colon SUVratio deserves further investigation.
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Affiliation(s)
| | - Ornella Cantale
- Department of OncologyUniversity of Turin, San Luigi HospitalTurinItaly
| | - Andrea Mogavero
- Department of OncologyUniversity of Turin, San Luigi HospitalTurinItaly
| | | | | | | | | | - Silvia Novello
- Department of OncologyUniversity of Turin, San Luigi HospitalTurinItaly
| | | | - Giuseppe Luigi Banna
- Candiolo Cancer Institute, FPO‐IRCCSTurinItaly
- Portsmouth Hospitals University NHS TrustPortsmouthUK
- Faculty of Science and HealthSchool of Pharmacy and Biomedical Sciences, University of PortsmouthPortsmouthUK
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Chiorino G, Petracci E, Sehovic E, Gregnanin I, Camussi E, Mello-Grand M, Ostano P, Riggi E, Vergini V, Russo A, Berrino E, Ortale A, Garena F, Venesio T, Gallo F, Favettini E, Frigerio A, Matullo G, Segnan N, Giordano L. Plasma microRNA ratios associated with breast cancer detection in a nested case-control study from a mammography screening cohort. Sci Rep 2023; 13:12040. [PMID: 37491482 PMCID: PMC10368693 DOI: 10.1038/s41598-023-38886-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 07/17/2023] [Indexed: 07/27/2023] Open
Abstract
Mammographic breast cancer screening is effective in reducing breast cancer mortality. Nevertheless, several limitations are known. Therefore, developing an alternative or complementary non-invasive tool capable of increasing the accuracy of the screening process is highly desirable. The objective of this study was to identify circulating microRNA (miRs) ratios associated with BC in women attending mammography screening. A nested case-control study was conducted within the ANDROMEDA cohort (women of age 46-67 attending BC screening). Pre-diagnostic plasma samples, information on life-styles and common BC risk factors were collected. Small-RNA sequencing was carried out on plasma samples from 65 cases and 66 controls. miR ratios associated with BC were selected by two-sample Wilcoxon test and lasso logistic regression. Subsequent assessment by RT-qPCR of the miRs contained in the selected miR ratios was carried out as a platform validation. To identify the most promising biomarkers, penalised logistic regression was further applied to candidate miR ratios alone, or in combination with non-molecular factors. Small-RNA sequencing yielded 20 candidate miR ratios associated with BC, which were further assessed by RT-qPCR. In the resulting model, penalised logistic regression selected seven miR ratios (miR-199a-3p_let-7a-5p, miR-26b-5p_miR-142-5p, let-7b-5p_miR-19b-3p, miR-101-3p_miR-19b-3p, miR-93-5p_miR-19b-3p, let-7a-5p_miR-22-3p and miR-21-5p_miR-23a-3p), together with body mass index (BMI), menopausal status (MS), the interaction term BMI * MS, life-style score and breast density. The ROC AUC of the model was 0.79 with a sensitivity and specificity of 71.9% and 76.6%, respectively. We identified biomarkers potentially useful for BC screening measured through a widespread and low-cost technique. This is the first study reporting circulating miRs for BC detection in a screening setting. Validation in a wider sample is warranted.Trial registration: The Andromeda prospective cohort study protocol was retrospectively registered on 27-11-2015 (NCT02618538).
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Affiliation(s)
- Giovanna Chiorino
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Via Malta 3, 13900, Biella, Italy
| | - Elisabetta Petracci
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Emir Sehovic
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Via Malta 3, 13900, Biella, Italy.
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.
| | - Ilaria Gregnanin
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Via Malta 3, 13900, Biella, Italy
| | - Elisa Camussi
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
| | - Maurizia Mello-Grand
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Via Malta 3, 13900, Biella, Italy
| | - Paola Ostano
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, Via Malta 3, 13900, Biella, Italy
| | - Emilia Riggi
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
| | - Viviana Vergini
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
| | - Alessia Russo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Enrico Berrino
- Department of Medical Sciences, University of Turin, Turin, Italy
- Pathology Unit, Candiolo Cancer Institute, FPO IRCCS, Candiolo, Italy
| | - Andrea Ortale
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
| | - Francesca Garena
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
| | - Tiziana Venesio
- Pathology Unit, Candiolo Cancer Institute, FPO IRCCS, Candiolo, Italy
| | - Federica Gallo
- Epidemiology Unit, Staff Health Direction, Local Health Authority 1 of Cuneo, Cuneo, Italy
| | | | - Alfonso Frigerio
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Nereo Segnan
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy.
| | - Livia Giordano
- SSD Epidemiologia Screening, CPO-AOU Città della Salute e della Scienza di Torino, Via Camillo Benso Di Cavour 31, 10123, Turin, Italy
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6
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Berrino E, Miglio U, Bellomo SE, Debernardi C, Bragoni A, Petrelli A, Cascardi E, Giordano S, Montemurro F, Marchiò C, Venesio T, Sapino A. The Tumor-Specific Expression of L1 Retrotransposons Independently Correlates with Time to Relapse in Hormone-Negative Breast Cancer Patients. Cells 2022; 11:cells11121944. [PMID: 35741073 PMCID: PMC9221920 DOI: 10.3390/cells11121944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/09/2022] [Accepted: 06/15/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Long-Interspersed Nuclear Element (L1) retrotransposons are silenced in healthy tissues but unrepressed in cancer. Even if L1 reactivation has been associated with reduced overall survival in breast cancer (BC) patients, a comprehensive correlation with clinicopathological features is still missing. METHODS Using quantitative, reverse-transcription PCR, we assessed L1 mRNA expression in 12 BC cells, 210 BC patients and in 47 normal mammary tissues. L1 expression was then correlated with molecular and clinicopathological data. RESULTS We identified a tumor-exclusive expression of L1s, absent in normal mammary cells and tissues. A positive correlation between L1 expression and tumor dedifferentiation, lymph-node involvement and increased immune infiltration was detected. Molecular subtyping highlighted an enrichment of L1s in basal-like cells and cancers. By exploring disease-free survival, we identified L1 overexpression as an independent biomarker for patients with a high risk of recurrence in hormone-receptor-negative BCs. CONCLUSIONS Overall, L1 reactivation identified BCs with aggressive features and patients with a worse clinical fate.
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Affiliation(s)
- Enrico Berrino
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy;
| | - Umberto Miglio
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
| | - Sara Erika Bellomo
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Oncology, University of Turin, 10124 Turin, Italy
| | - Carla Debernardi
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy;
| | - Alberto Bragoni
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy;
| | - Annalisa Petrelli
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
| | - Eliano Cascardi
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy;
| | - Silvia Giordano
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Oncology, University of Turin, 10124 Turin, Italy
| | - Filippo Montemurro
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
| | - Caterina Marchiò
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy;
| | - Tiziana Venesio
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Correspondence: ; Tel.: +39-011-9933547; Fax: +39-011-9933480
| | - Anna Sapino
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (E.B.); (U.M.); (S.E.B.); (A.B.); (A.P.); (E.C.); (S.G.); (F.M.); (C.M.); (A.S.)
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy;
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7
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Debernardi C, Libera L, Berrino E, Sahnane N, Chiaravalli AM, Laudi C, Berselli M, Sapino A, Sessa F, Venesio T, Furlan D. Correction to: Evaluation of global and intragenic hypomethylation in colorectal adenomas improves patient stratification and colorectal cancer risk prediction. Clin Epigenetics 2021; 13:178. [PMID: 34548107 PMCID: PMC8456621 DOI: 10.1186/s13148-021-01166-7] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Carla Debernardi
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Laura Libera
- Pathology Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Enrico Berrino
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Torino, Torino, Italy
| | - Nora Sahnane
- Pathology Unit, ASST Sette Laghi, Varese, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Anna Maria Chiaravalli
- Pathology Unit, ASST Sette Laghi, Varese, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Cristiana Laudi
- Gastroenterology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Mattia Berselli
- Surgical Oncology and Minimally Invasive Unit, Department of Surgery, ASST Sette Laghi, Varese, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Anna Sapino
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Torino, Torino, Italy
| | - Fausto Sessa
- Pathology Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Tiziana Venesio
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.
| | - Daniela Furlan
- Pathology Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
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8
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Petrelli A, Bellomo SE, Sarotto I, Kubatzki F, Sgandurra P, Maggiorotto F, Di Virgilio MR, Ponzone R, Geuna E, Galizia D, Nuzzo AM, Medico E, Miglio U, Berrino E, Venesio T, Ribisi S, Provero P, Sapino A, Giordano S, Montemurro F. MiR-100 is a predictor of endocrine responsiveness and prognosis in patients with operable luminal breast cancer. ESMO Open 2021; 5:e000937. [PMID: 33122354 PMCID: PMC7597498 DOI: 10.1136/esmoopen-2020-000937] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Overexpression of miR-100 in stem cells derived from basal-like breast cancers causes loss of stemness, induction of luminal breast cancer markers and response to endocrine therapy. We, therefore, explored miR-100 as a novel biomarker in patients with luminal breast cancer. METHODS miR-100 expression was studied in 90 patients with oestrogen-receptor-positive/human-epidermal growth factor receptor 2-negative breast cancer enrolled in a prospective study of endocrine therapy given either preoperatively, or for the treatment of de novo metastatic disease. Response was defined as a Ki67 ≤2.7% after 21±3 days of treatment. The prognostic role of miR-100 expression was evaluated in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) and The Cancer Genome Atlas (TCGA) breast cancer datasets. Additionally, we explored the correlation between miR-100 and the expression its targets reported as being associated with endocrine resistance. Finally, we evaluated whether a signature based on miR-100 and its target genes could predict the luminal A molecular subtype. RESULTS Baseline miR-100 was significantly anticorrelated with baseline and post-treatment Ki67 (p<0.001 and 0.004, respectively), and independently associated with response to treatment (OR 3.329, p=0.047). In the METABRIC dataset, high expression of miR-100 identified women with luminal A tumours treated with adjuvant endocrine therapy with improved overall survival (HR 0.55, p<0.001). miR-100 was negatively correlated with PLK1, FOXA1, mTOR and IGF1R expression, potentially explaining its prognostic effect. Finally, a miR-100-based signature developed in patients enrolled in the prospective study outperformed Ki67 alone in predicting the luminal A phenotype. CONCLUSIONS Our findings suggest that miR-100 should be further explored as a biomarker in patients with luminal breast cancer.
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Affiliation(s)
- Annalisa Petrelli
- Cancer Molecular Biology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | | | - Ivana Sarotto
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Franziska Kubatzki
- Gynaecological Oncology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Paola Sgandurra
- Gynaecological Oncology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Furio Maggiorotto
- Gynaecological Oncology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | | | - Riccardo Ponzone
- Gynaecological Oncology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Elena Geuna
- Multidisciplinary Outpatient Oncology Clinic, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Danilo Galizia
- Multidisciplinary Outpatient Oncology Clinic, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Anna Maria Nuzzo
- Clinical Research Office, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Enzo Medico
- Department of Oncology, University of Turin, Torino, Italy; Oncogenomics Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Umberto Miglio
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Enrico Berrino
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy; Department of Medical Sciences, University of Turin, Torino, Italy
| | - Tiziana Venesio
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Salvatore Ribisi
- Cancer Molecular Biology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Paolo Provero
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy; Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Anna Sapino
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy; Department of Medical Sciences, University of Turin, Torino, Italy
| | - Silvia Giordano
- Cancer Molecular Biology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy; Department of Oncology, University of Turin, Torino, Italy
| | - Filippo Montemurro
- Multidisciplinary Outpatient Oncology Clinic, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.
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9
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Debernardi C, Libera L, Berrino E, Sahnane N, Chiaravalli AM, Laudi C, Berselli M, Sapino A, Sessa F, Venesio T, Furlan D. Evaluation of global and intragenic hypomethylation in colorectal adenomas improves patient stratification and colorectal cancer risk prediction. Clin Epigenetics 2021; 13:154. [PMID: 34372923 PMCID: PMC8351348 DOI: 10.1186/s13148-021-01135-0] [Citation(s) in RCA: 10] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/15/2021] [Indexed: 12/16/2022] Open
Abstract
Background Aberrant DNA hypomethylation of the long interspersed nuclear elements (LINE-1 or L1) has been recognized as an early event of colorectal transformation. Simultaneous genetic and epigenetic analysis of colorectal adenomas may be an effective and rapid strategy to identify key biological features leading to accelerated colorectal tumorigenesis. In particular, global and/or intragenic LINE-1 hypomethylation of adenomas may represent a helpful tool for improving colorectal cancer (CRC) risk stratification of patients after surgical removal of polyps. To verify this hypothesis, we analyzed a cohort of 102 adenomas derived from 40 high-risk patients (who developed CRC in a post-polypectomy of at least one year) and 43 low-risk patients (who did not develop CRC in a post-polypectomy of at least 5 years) for their main pathological features, the presence of hotspot variants in driver oncogenes (KRAS, NRAS, BRAF and PIK3CA), global (LINE-1) and intragenic (L1-MET) methylation status. Results In addition to a significantly higher adenoma size and an older patients’ age, adenomas from high-risk patients were more hypomethylated than those from low-risk patients for both global and intragenic LINE-1 assays. DNA hypomethylation, measured by pyrosequencing, was independent from other parameters, including the presence of oncogenic hotspot variants detected by mass spectrometry. Combining LINE-1 and L1-MET analyses and profiling the samples according to the presence of at least one hypomethylated assay improved the discrimination between high and low risk lesions (p = 0.005). Remarkably, adenomas with at least one hypomethylated assay identified the patients with a significantly (p < 0.001) higher risk of developing CRC. Multivariable analysis and logistic regression evaluated by the ROC curves proved that methylation status was an independent variable improving cancer risk prediction (p = 0.02). Conclusions LINE-1 and L1-MET hypomethylation in colorectal adenomas are associated with a higher risk of developing CRC. DNA global and intragenic hypomethylation are independent markers that could be used in combination to successfully improve the stratification of patients who enter a colonoscopy surveillance program. Graphic abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01135-0.
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Affiliation(s)
- Carla Debernardi
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Laura Libera
- Pathology Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Enrico Berrino
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Torino, Torino, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Nora Sahnane
- Pathology Unit, ASST Sette Laghi, Varese, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Anna Maria Chiaravalli
- Pathology Unit, ASST Sette Laghi, Varese, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Cristiana Laudi
- Gastroenterology, Candiolo Cancer Institute, Candiolo, Italy
| | - Mattia Berselli
- Surgical Oncology and Minimally Invasive Unit, Department of Surgery, ASST Sette Laghi, Varese, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Anna Sapino
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Torino, Torino, Italy
| | - Fausto Sessa
- Pathology Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Tiziana Venesio
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy. .,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy.
| | - Daniela Furlan
- Pathology Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
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10
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Scatolini M, Patel A, Grosso E, Mello-Grand M, Ostano P, Coppo R, Vitiello M, Venesio T, Zaccagna A, Pisacane A, Sarotto I, Taverna D, Poliseno L, Bergamaschi D, Chiorino G. GJB5 association with BRAF mutation and survival in cutaneous malignant melanoma. Br J Dermatol 2021; 186:117-128. [PMID: 34240406 DOI: 10.1111/bjd.20629] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND Gap junctional intercellular communication is crucial for epidermal cellular homeostasis. Inability to establish melanocyte-keratinocytes contacts and loss of intercellular junction's integrity may contribute to melanoma development. Connexins, laminins and desmocollins have been implicated in the control of melanoma growth, where their reduced expression has been reported in metastatic lesions. OBJECTIVES The aim of this study was to investigate Connexin 31.1 (GJB5) expression and identify any association with BRAF mutational status, melanoma patient prognosis and MAPK inhibitors (MAPKi) treatment. MATERIAL AND METHODS GJB5 expression was measured at RNA and protein level in melanoma clinical samples and established cell lines treated or not with BRAF and MEK inhibitors, as well as in cell lines which developed MAPK inhibitors resistance. Findings were further validated and confirmed by analysis of independent datasets. RESULTS Our analysis reveals significant downregulation of GJB5 expression in metastatic melanoma lesions compared to primary ones and in BRAF mutated versus BRAF wild-type melanomas. Likewise, GJB5 expression is significantly lower in BRAFV600E compared with BRAFWT cell lines and increases upon MAPKi treatment. MAPKi-resistant melanoma cells display a similar expression pattern compared to BRAFWT cells, with increased GJB5 expression associated with morphological changes. Enhancement of BRAFV600E expression in BRAFWT melanoma cells significantly upregulates miR-335-5p expression with consequent downregulation of GJB5, one of its targets. Furthermore, overexpression of miR-335-5p in two BRAFWT cell lines confirms specific GJB5 protein downregulation. RT-qPCR analysis also revealed upregulation of miR-335 in BRAFV600E melanoma cells, which is significantly downregulated in cells resistant to MEK inhibitors. Our data were further validated using the TCGA-SKCM dataset, where BRAF mutations associate with increased miR-335 expression and inversely correlate with GJB5 expression. In clinical samples, GJB5 underexpression is also associated with patient overall worse survival, especially at early stages. CONCLUSION We identified a significant association between metastases / BRAF mutation and low GJB5 expression in melanoma. Our results identify a novel mechanism of Gap-junctional protein regulation, suggesting a prognostic role for GJB5 in cutaneous melanoma.
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Affiliation(s)
- M Scatolini
- Molecular Oncology Laboratory, Fondazione Edo ed Elvo Tempia, 13875, Ponderano, BI, Italy
| | - A Patel
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London SMD, QMUL, London, E1 2AT, UK
| | - E Grosso
- Molecular Oncology Laboratory, Fondazione Edo ed Elvo Tempia, 13875, Ponderano, BI, Italy
| | - M Mello-Grand
- Cancer Genomics Laboratory, Fondazione Edo ed Elvo Tempia, 13900, Biella, Italy
| | - P Ostano
- Cancer Genomics Laboratory, Fondazione Edo ed Elvo Tempia, 13900, Biella, Italy
| | - R Coppo
- Molecular Biotechnology Centre, 10126, Torino, Italy.,Department of Clinical Bio-Resource Research and Development, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - M Vitiello
- Oncogenomics Unit, Core Research Laboratory, Istituto Toscano Tumori, Institute of Clinical Physiology, CNR, 56124, Pisa, Italy
| | - T Venesio
- Pathology and Dermosurgery Units, Candiolo Cancer Institute (FPO-IRCCS), 10060, Candiolo, Turin, Italy
| | - A Zaccagna
- Pathology and Dermosurgery Units, Candiolo Cancer Institute (FPO-IRCCS), 10060, Candiolo, Turin, Italy
| | - A Pisacane
- Pathology and Dermosurgery Units, Candiolo Cancer Institute (FPO-IRCCS), 10060, Candiolo, Turin, Italy
| | - I Sarotto
- Pathology and Dermosurgery Units, Candiolo Cancer Institute (FPO-IRCCS), 10060, Candiolo, Turin, Italy
| | - D Taverna
- Molecular Biotechnology Centre, 10126, Torino, Italy
| | - L Poliseno
- Oncogenomics Unit, Core Research Laboratory, Istituto Toscano Tumori, Institute of Clinical Physiology, CNR, 56124, Pisa, Italy
| | - D Bergamaschi
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London SMD, QMUL, London, E1 2AT, UK
| | - G Chiorino
- Cancer Genomics Laboratory, Fondazione Edo ed Elvo Tempia, 13900, Biella, Italy
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11
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Berrino E, Balsamo A, Pisacane A, Gallo S, Becco P, Miglio U, Caravelli D, Poletto S, Paruzzo L, Debernardi C, Piccinelli C, Zaccagna A, Rescigno P, Aglietta M, Sapino A, Carnevale-Schianca F, Venesio T. High BRAF variant allele frequencies are associated with distinct pathological features and responsiveness to target therapy in melanoma patients. ESMO Open 2021; 6:100133. [PMID: 33984673 PMCID: PMC8134716 DOI: 10.1016/j.esmoop.2021.100133] [Citation(s) in RCA: 10] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/02/2021] [Accepted: 04/08/2021] [Indexed: 12/20/2022] Open
Abstract
Background BRAF mutant melanoma patients are commonly treated with anti-BRAF therapeutic strategies. However, many factors, including the percentage of BRAF-mutated cells, may contribute to the great variability in patient outcomes. Patients and methods The BRAF variant allele frequency (VAF; defined as the percentage of mutated alleles) of primary and secondary melanoma lesions, obtained from 327 patients with different disease stages, was assessed by pyrosequencing. The BRAF mutation rate and VAF were then correlated with melanoma pathological features and patients’ clinical characteristics. Kaplan–Meier curves were used to study the correlations between BRAF VAF, overall survival (OS), and progression-free survival (PFS) in a subset of 62 patients treated by anti-BRAF/anti-MEK therapy after metastatic progression. Results A highly heterogeneous BRAF VAF was identified (3%-90%). Besides being correlated with age, a higher BRAF VAF level was related to moderate lymphocytic infiltration (P = 0.017), to melanoma thickness according to Clark levels, (level V versus III, P = 0.004; level V versus IV, P = 0.04), to lymph node metastases rather than cutaneous (P = 0.04) or visceral (P = 0.03) secondary lesions. In particular, a BRAF VAF >25% was significantly associated with a favorable outcome in patients treated with the combination of anti-BRAF/anti-MEK drug (OS P = 0.04; PFS P = 0.019), retaining a significant value as an independent factor for the OS and the PFS in the multivariate analysis (P = 0.014 and P = 0.003, respectively). Conclusion These results definitively support the role of the BRAF VAF as a potential prognostic and predictive biomarker in melanoma patients in the context of BRAF inhibition. In melanoma the response to anti-BRAF targeted therapies is heterogeneous and influenced by several features. The role of the BRAF VAF as provider of sensitivity to target therapies is debated. We found that high BRAF VAFs are associated with patient age, melanoma thickness, non-brisk TILs and lymph node metastases. We proved the independent prognostic value of high BRAF VAFs in melanoma patients treated with targeted therapies. The quantitative evaluation of BRAF mutations allows stratifying melanoma patients to the BRAF/MEK targeted treatment.
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Affiliation(s)
- E Berrino
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy; Department of Medical Sciences, University of Turin, Turin, Italy
| | - A Balsamo
- Clinical Research Office, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy
| | - A Pisacane
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy
| | - S Gallo
- Medical Oncology Division, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy
| | - P Becco
- Medical Oncology Division, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy
| | - U Miglio
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy
| | - D Caravelli
- Medical Oncology Division, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy
| | - S Poletto
- Medical Oncology Division, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy; Department of Oncology, University of Turin, Turin, Italy
| | - L Paruzzo
- Medical Oncology Division, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy; Department of Oncology, University of Turin, Turin, Italy
| | - C Debernardi
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy
| | - C Piccinelli
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy
| | - A Zaccagna
- Dermosurgery, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy
| | - P Rescigno
- Interdisciplinary Group for Research and Clinical Trials, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy
| | - M Aglietta
- Medical Oncology Division, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy; Department of Oncology, University of Turin, Turin, Italy
| | - A Sapino
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy; Department of Medical Sciences, University of Turin, Turin, Italy.
| | | | - T Venesio
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy.
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D'Ambrosio C, Erriquez J, Arigoni M, Capellero S, Mittica G, Ghisoni E, Borella F, Katsaros D, Privitera S, Ribotta M, Maldi E, Nardo GD, Berrino E, Venesio T, Ponzone R, Vaira M, Hall D, Jimenez-Linan M, Paterson A, Valabrega G, Calogero R, Brenton J, Di Renzo M, Olivero M. Abstract 1677: Assays of conventional chemotherapeutics and targeted drugs for ovarian cancer using patient derived models. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1677] [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
Patients with advanced ovarian cancers have experienced little improvement in overall survival with standard treatments. We used patient derived models to accelerate the discovery of treatment options. We developed a platform of Patient Derived Xenografts (PDX), by implanting and propagating patient's tumor samples collected at surgery in severely immunocompromised mice. From each PDX line we derived short term cultures of PDX Derived Tumor Cells (PDTCs). We envisioned that the weakness of PDXs and PDTCs, i.e. lack of human stromal and immune cells, might be instrumental to link tumor biomarkers to treatments. We have successfully propagated 49 PDX lines from metastatic EOC, which were fully characterized as far as histology, immunohistochemistry of epithelial and tissue specific markers and presence of TP53 and BRCA1/2 mutations. On PDTCs cultures we first assessed sensitivity to Carboplatin, currently used as first-line drug in ovarian cancer treatment. Of PDX lines derived from naïve metastatic HGS-EOC copy number variations and whole exome sequencing analyses were carried out, in order to identify putative and actionable cancer genes. Thus, on PDTCs we assayed also approved or experimental targeted drugs as monotherapy or in combinations. In one PDX line we identified a possibly loss-of-function mutation (W624R) of the PIK3R1 gene (encoding the p85alpha regulatory subunit of PI3K) with an allele frequency of 0.9, which could result in activation of the PI3K pathway. Several PI3K inhibitors were assayed on PDTCs of this PDX line harboring the PIK3R1W624R. Buparlisib (a Pan Class I PI3Ki) showed the ability to block proliferation of the PDTCs and the growth of the relevant PDXs in vivo.
Altogether these data show that Patient Derived models are invaluable tools to unveil actionable pathways for the treatment of advanced/metastatic HGS-EOC.
Citation Format: Concetta D'Ambrosio, Jessica Erriquez, Maddalena Arigoni, Sonia Capellero, Gloria Mittica, Eleonora Ghisoni, Fulvio Borella, Dionyssios Katsaros, Silvana Privitera, Marisa Ribotta, Elena Maldi, Giovanna Di Nardo, Enrico Berrino, Tiziana Venesio, Riccardo Ponzone, Marco Vaira, Douglas Hall, Mercedes Jimenez-Linan, Anna Paterson, Giorgio Valabrega, Raffaele Calogero, James Brenton, Mariaflavia Di Renzo, Martina Olivero. Assays of conventional chemotherapeutics and targeted drugs for ovarian cancer using patient derived models [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1677.
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Affiliation(s)
| | | | | | | | | | | | - Fulvio Borella
- 4Citta della Salute e della Scienza di Torino, Torino, Italy
| | | | | | - Marisa Ribotta
- 4Citta della Salute e della Scienza di Torino, Torino, Italy
| | - Elena Maldi
- 2Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
| | | | | | | | | | - Marco Vaira
- 2Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
| | - Douglas Hall
- 6University of Cambridge, Cambridge, CB2 0RE, United Kingdom
| | | | - Anna Paterson
- 7Cancer Research UK Cambridge Institute, Cambridge, CB2 0RE UK, United Kingdom
| | | | | | - James Brenton
- 7Cancer Research UK Cambridge Institute, Cambridge, CB2 0RE UK, United Kingdom
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13
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Berrino E, Annaratone L, Miglio U, Maldi E, Piccinelli C, Peano E, Balmativola D, Cassoni P, Pisacane A, Sarotto I, Venesio T, Sapino A, Marchiò C. Cold Formalin Fixation Guarantees DNA Integrity in Formalin Fixed Paraffin Embedded Tissues: Premises for a Better Quality of Diagnostic and Experimental Pathology With a Specific Impact on Breast Cancer. Front Oncol 2020; 10:173. [PMID: 32140450 PMCID: PMC7042205 DOI: 10.3389/fonc.2020.00173] [Citation(s) in RCA: 16] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 01/31/2020] [Indexed: 11/29/2022] Open
Abstract
Formalin fixation and paraffin embedding (FFPE) represent the standard method to preserve tissue specimens for diagnostic pathology, however formalin fixation induces severe fragmentation of nucleic acids. We investigated whether formalin fixation at 4°C could preserve DNA integrity in FFPE specimens. Paired samples from 38 specimens were formalin fixed at room temperature (stdFFPE) and at 4°C (coldFFPE), respectively. Two independent cohorts were prospectively collected, cohort A (collected 6 years prior to the study, n = 21), cohort B (collected at time of the study, n = 17). DNA was extracted and its integrity evaluated with a qPCR-based assay that produces a normalized integrity index, the QC score (ratio between the quantity of a long and a short amplicon of the same gene). We observed higher QC scores in coldFFPE compared to stdFFPE samples (mean values: 0.69 vs. 0.36, p < 0.0001) and stdFFPE breast cancer specimens showed the most detrimental effect overall. Comparable QC scores were obtained between coldFFPE tissues of both cohorts; conversely, DNA integrity of stdFFPE was significantly lower in cohort A compared to cohort B (p < 0.0001). Of note, QC scores of stdFFPE (but not of coldFFPE) samples were significantly reduced following 6 months of storage (p = 0.0001). Monitored formalin fixation at 4°C outperforms standard fixation in ensuring high-quality DNA, which is key to feasibility of downstream high-throughput molecular analyses. An important effect was observed over storage time, thus suggesting a likely better preservation of archival samples when this cold fixation protocol is used.
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Affiliation(s)
- Enrico Berrino
- Department of Medical Sciences, University of Turin, Turin, Italy.,Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Laura Annaratone
- Department of Medical Sciences, University of Turin, Turin, Italy.,Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Umberto Miglio
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Elena Maldi
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Chiara Piccinelli
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Erica Peano
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | | | - Paola Cassoni
- Department of Medical Sciences, University of Turin, Turin, Italy.,Pathology Unit, Città Della Salute e Della Scienza di Torino, Turin, Italy
| | - Alberto Pisacane
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Ivana Sarotto
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Tiziana Venesio
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Anna Sapino
- Department of Medical Sciences, University of Turin, Turin, Italy.,Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin, Turin, Italy.,Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
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14
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D’Ambrosio C, Erriquez J, Arigoni M, Capellero S, Mittica G, Ghisoni E, Borella F, Katsaros D, Privitera S, Ribotta M, Maldi E, Di Nardo G, Berrino E, Venesio T, Ponzone R, Vaira M, Hall D, Jimenez-Linan M, Paterson AL, Calogero RA, Brenton JD, Valabrega G, Di Renzo MF, Olivero M. PIK3R1W624R Is an Actionable Mutation in High Grade Serous Ovarian Carcinoma. Cells 2020; 9:E442. [PMID: 32075097 PMCID: PMC7072782 DOI: 10.3390/cells9020442] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/04/2020] [Accepted: 02/13/2020] [Indexed: 12/17/2022] Open
Abstract
Identifying cancer drivers and actionable mutations is critical for precision oncology. In epithelial ovarian cancer (EOC) the majority of mutations lack biological or clinical validation. We fully characterized 43 lines of Patient-Derived Xenografts (PDXs) and performed copy number analysis and whole exome sequencing of 12 lines derived from naïve, high grade EOCs. Pyrosequencing allowed quantifying mutations in the source tumours. Drug response was assayed on PDX Derived Tumour Cells (PDTCs) and in vivo on PDXs. We identified a PIK3R1W624R variant in PDXs from a high grade serous EOC. Allele frequencies of PIK3R1W624R in all the passaged PDXs and in samples of the source tumour suggested that it was truncal and thus possibly a driver mutation. After inconclusive results in silico analyses, PDTCs and PDXs allowed the showing actionability of PIK3R1W624R and addiction of PIK3R1W624R carrying cells to inhibitors of the PI3K/AKT/mTOR pathway. It is noteworthy that PIK3R1 encodes the p85α regulatory subunit of PI3K, that is very rarely mutated in EOC. The PIK3R1W624R mutation is located in the cSH2 domain of the p85α that has never been involved in oncogenesis. These data show that patient-derived models are irreplaceable in their role of unveiling unpredicted driver and actionable variants in advanced ovarian cancer.
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Affiliation(s)
- Concetta D’Ambrosio
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, 10060 Torino, Italy; (C.D.); (J.E.); (S.C.); (G.M.); (E.G.); (E.M.); (E.B.); (T.V.); (R.P.); (M.V.); (G.V.); (M.O.)
- Department of Oncology, University of Torino, Candiolo, 10060 Torino, Italy
| | - Jessica Erriquez
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, 10060 Torino, Italy; (C.D.); (J.E.); (S.C.); (G.M.); (E.G.); (E.M.); (E.B.); (T.V.); (R.P.); (M.V.); (G.V.); (M.O.)
| | - Maddalena Arigoni
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126 Torino, Italy; (M.A.); (R.A.C.)
| | - Sonia Capellero
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, 10060 Torino, Italy; (C.D.); (J.E.); (S.C.); (G.M.); (E.G.); (E.M.); (E.B.); (T.V.); (R.P.); (M.V.); (G.V.); (M.O.)
- Department of Oncology, University of Torino, Candiolo, 10060 Torino, Italy
| | - Gloria Mittica
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, 10060 Torino, Italy; (C.D.); (J.E.); (S.C.); (G.M.); (E.G.); (E.M.); (E.B.); (T.V.); (R.P.); (M.V.); (G.V.); (M.O.)
| | - Eleonora Ghisoni
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, 10060 Torino, Italy; (C.D.); (J.E.); (S.C.); (G.M.); (E.G.); (E.M.); (E.B.); (T.V.); (R.P.); (M.V.); (G.V.); (M.O.)
| | - Fulvio Borella
- Città della Salute e della Scienza, 10126 Torino, Italy; (F.B.); (D.K.); (S.P.); (M.R.)
| | - Dionyssios Katsaros
- Città della Salute e della Scienza, 10126 Torino, Italy; (F.B.); (D.K.); (S.P.); (M.R.)
| | - Silvana Privitera
- Città della Salute e della Scienza, 10126 Torino, Italy; (F.B.); (D.K.); (S.P.); (M.R.)
| | - Marisa Ribotta
- Città della Salute e della Scienza, 10126 Torino, Italy; (F.B.); (D.K.); (S.P.); (M.R.)
| | - Elena Maldi
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, 10060 Torino, Italy; (C.D.); (J.E.); (S.C.); (G.M.); (E.G.); (E.M.); (E.B.); (T.V.); (R.P.); (M.V.); (G.V.); (M.O.)
| | - Giovanna Di Nardo
- Department of Life Sciences and Systems Biology, University of Torino, 10125 Torino, Italy;
| | - Enrico Berrino
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, 10060 Torino, Italy; (C.D.); (J.E.); (S.C.); (G.M.); (E.G.); (E.M.); (E.B.); (T.V.); (R.P.); (M.V.); (G.V.); (M.O.)
- Department of Medical Sciences, University of Torino, 10126 Torino, Italy
| | - Tiziana Venesio
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, 10060 Torino, Italy; (C.D.); (J.E.); (S.C.); (G.M.); (E.G.); (E.M.); (E.B.); (T.V.); (R.P.); (M.V.); (G.V.); (M.O.)
| | - Riccardo Ponzone
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, 10060 Torino, Italy; (C.D.); (J.E.); (S.C.); (G.M.); (E.G.); (E.M.); (E.B.); (T.V.); (R.P.); (M.V.); (G.V.); (M.O.)
| | - Marco Vaira
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, 10060 Torino, Italy; (C.D.); (J.E.); (S.C.); (G.M.); (E.G.); (E.M.); (E.B.); (T.V.); (R.P.); (M.V.); (G.V.); (M.O.)
| | - Douglas Hall
- University of Cambridge, Cambridge CB2 0XZ, UK; (D.H.); (M.J.-L.); (A.L.P.); (J.D.B.)
- Cancer Research UK Cambridge Institute, Cambridge CB2 0RE, UK
| | | | - Anna L. Paterson
- University of Cambridge, Cambridge CB2 0XZ, UK; (D.H.); (M.J.-L.); (A.L.P.); (J.D.B.)
- Cancer Research UK Cambridge Institute, Cambridge CB2 0RE, UK
| | - Raffaele A. Calogero
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126 Torino, Italy; (M.A.); (R.A.C.)
| | - James D. Brenton
- University of Cambridge, Cambridge CB2 0XZ, UK; (D.H.); (M.J.-L.); (A.L.P.); (J.D.B.)
- Cancer Research UK Cambridge Institute, Cambridge CB2 0RE, UK
| | - Giorgio Valabrega
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, 10060 Torino, Italy; (C.D.); (J.E.); (S.C.); (G.M.); (E.G.); (E.M.); (E.B.); (T.V.); (R.P.); (M.V.); (G.V.); (M.O.)
- Department of Oncology, University of Torino, Candiolo, 10060 Torino, Italy
| | - Maria Flavia Di Renzo
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, 10060 Torino, Italy; (C.D.); (J.E.); (S.C.); (G.M.); (E.G.); (E.M.); (E.B.); (T.V.); (R.P.); (M.V.); (G.V.); (M.O.)
- Department of Oncology, University of Torino, Candiolo, 10060 Torino, Italy
| | - Martina Olivero
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, 10060 Torino, Italy; (C.D.); (J.E.); (S.C.); (G.M.); (E.G.); (E.M.); (E.B.); (T.V.); (R.P.); (M.V.); (G.V.); (M.O.)
- Department of Oncology, University of Torino, Candiolo, 10060 Torino, Italy
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15
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Ciavarella S, Vegliante MC, Fabbri M, De Summa S, Melle F, Motta G, De Iuliis V, Opinto G, Enjuanes A, Rega S, Gulino A, Agostinelli C, Scattone A, Tommasi S, Mangia A, Mele F, Simone G, Zito AF, Ingravallo G, Vitolo U, Chiappella A, Tarella C, Gianni AM, Rambaldi A, Zinzani PL, Casadei B, Derenzini E, Loseto G, Pileri A, Tabanelli V, Fiori S, Rivas-Delgado A, López-Guillermo A, Venesio T, Sapino A, Campo E, Tripodo C, Guarini A, Pileri SA. Dissection of DLBCL microenvironment provides a gene expression-based predictor of survival applicable to formalin-fixed paraffin-embedded tissue. Ann Oncol 2019; 30:2015. [PMID: 31539020 PMCID: PMC6938597 DOI: 10.1093/annonc/mdz386] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- S Ciavarella
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - M C Vegliante
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - M Fabbri
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan
| | - S De Summa
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - F Melle
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan
| | - G Motta
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan
| | - V De Iuliis
- Post-graduated Medical School of Clinical Pathology, "Gabriele D'Annunzio", University of Chieti, Chieti
| | - G Opinto
- Functional Biomorphology Laboratory, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - A Enjuanes
- Unitat de Genòmica, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona; CIBERONC, Barcelona, Spain
| | - S Rega
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - A Gulino
- Tumor Immunology Unit, Dipartimento per la Promozione della Salute e Materno Infantile "G. D'Alessandro", University of Palermo, Palermo
| | - C Agostinelli
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), Bologna University School of Medicine, Bologna
| | - A Scattone
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - S Tommasi
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - A Mangia
- Functional Biomorphology Laboratory, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - F Mele
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - G Simone
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - A F Zito
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - G Ingravallo
- Pathology Section, Department of Emergency and Organ Transplantation (DETO), University of Bari "Aldo Moro", Bari
| | - U Vitolo
- Department of Hematology, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Torino
| | - A Chiappella
- Department of Hematology, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Torino
| | - C Tarella
- Onco-Hematology Unit, European Institute of Oncology, IRCCS, Milan
| | - A M Gianni
- Onco-Hematology Unit, European Institute of Oncology, IRCCS, Milan
| | - A Rambaldi
- Department of Hematology and Oncology, Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII, Bergamo; School of Medicine, University of Milan, Milan, Italy
| | - P L Zinzani
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), Bologna University School of Medicine, Bologna
| | - B Casadei
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), Bologna University School of Medicine, Bologna
| | - E Derenzini
- Onco-Hematology Unit, European Institute of Oncology, IRCCS, Milan
| | - G Loseto
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - A Pileri
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), Bologna University School of Medicine, Bologna
| | - V Tabanelli
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan
| | - S Fiori
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan
| | - A Rivas-Delgado
- CIBERONC, Barcelona, Spain; Hematology Department, Hospital Clínic, Barcelona; IDIBAPS, Barcelona, Spain
| | - A López-Guillermo
- CIBERONC, Barcelona, Spain; Hematology Department, Hospital Clínic, Barcelona; IDIBAPS, Barcelona, Spain
| | - T Venesio
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - A Sapino
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy; Department of Medical Sciences, University of Torino, Turin, Italy
| | - E Campo
- CIBERONC, Barcelona, Spain; Haematopathology Unit, Pathology Department, Hospital Clínic, Barcelona; University of Barcelona, Barcelona, Spain
| | - C Tripodo
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - A Guarini
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - S A Pileri
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan
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16
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Ciavarella S, Vegliante MC, Fabbri M, De Summa S, Melle F, Motta G, De Iuliis V, Opinto G, Enjuanes A, Rega S, Gulino A, Agostinelli C, Scattone A, Tommasi S, Mangia A, Mele F, Simone G, Zito AF, Ingravallo G, Vitolo U, Chiappella A, Tarella C, Gianni AM, Rambaldi A, Zinzani PL, Casadei B, Derenzini E, Loseto G, Pileri A, Tabanelli V, Fiori S, Rivas-Delgado A, López-Guillermo A, Venesio T, Sapino A, Campo E, Tripodo C, Guarini A, Pileri SA. Dissection of DLBCL microenvironment provides a gene expression-based predictor of survival applicable to formalin-fixed paraffin-embedded tissue. Ann Oncol 2019; 29:2363-2370. [PMID: 30307529 PMCID: PMC6311951 DOI: 10.1093/annonc/mdy450] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [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: 12/12/2022] Open
Abstract
Background Gene expression profiling (GEP) studies recognized a prognostic role for tumor microenvironment (TME) in diffuse large B-cell lymphoma (DLBCL), but the routinely adoption of prognostic stromal signatures remains limited. Patients and methods Here, we applied the computational method CIBERSORT to generate a 1028-gene matrix incorporating signatures of 17 immune and stromal cytotypes. Then, we carried out a deconvolution on publicly available GEP data of 482 untreated DLBCLs to reveal associations between clinical outcomes and proportions of putative tumor-infiltrating cell types. Forty-five genes related to peculiar prognostic cytotypes were selected and their expression digitally quantified by NanoString technology on a validation set of 175 formalin-fixed, paraffin-embedded DLBCLs from two randomized trials. Data from an unsupervised clustering analysis were used to build a model of clustering assignment, whose prognostic value was also assessed on an independent cohort of 40 cases. All tissue samples consisted of pretreatment biopsies of advanced-stage DLBCLs treated by comparable R-CHOP/R-CHOP-like regimens. Results In silico analysis demonstrated that higher proportion of myofibroblasts (MFs), dendritic cells, and CD4+ T cells correlated with better outcomes and the expression of genes in our panel is associated with a risk of overall and progression-free survival. In a multivariate Cox model, the microenvironment genes retained high prognostic performance independently of the cell-of-origin (COO), and integration of the two prognosticators (COO + TME) improved survival prediction in both validation set and independent cohort. Moreover, the major contribution of MF-related genes to the panel and Gene Set Enrichment Analysis suggested a strong influence of extracellular matrix determinants in DLBCL biology. Conclusions Our study identified new prognostic categories of DLBCL, providing an easy-to-apply gene panel that powerfully predicts patients’ survival. Moreover, owing to its relationship with specific stromal and immune components, the panel may acquire a predictive relevance in clinical trials exploring new drugs with known impact on TME.
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Affiliation(s)
- S Ciavarella
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - M C Vegliante
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - M Fabbri
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan, Italy
| | - S De Summa
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - F Melle
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan, Italy
| | - G Motta
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan, Italy
| | - V De Iuliis
- Post-graduated Medical School of Clinical Pathology, "Gabriele D'Annunzio", University of Chieti, Chieti, Italy
| | - G Opinto
- Functional Biomorphology Laboratory, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - A Enjuanes
- Unitat de Genòmica, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; CIBERONC, Barcelona, Spain
| | - S Rega
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - A Gulino
- Tumor Immunology Unit, Dipartimento per la Promozione della Salute e Materno Infantile "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - C Agostinelli
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), Bologna University School of Medicine, Bologna, Italy
| | - A Scattone
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - S Tommasi
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - A Mangia
- Functional Biomorphology Laboratory, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - F Mele
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - G Simone
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - A F Zito
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - G Ingravallo
- Pathology Section, Department of Emergency and Organ Transplantation (DETO), University of Bari "Aldo Moro", Bari, Italy
| | - U Vitolo
- Department of Hematology, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Torino, Italy
| | - A Chiappella
- Department of Hematology, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Torino, Italy
| | - C Tarella
- Onco-Hematology Unit, European Institute of Oncology, IRCCS, Milan, Italy
| | - A M Gianni
- Onco-Hematology Unit, European Institute of Oncology, IRCCS, Milan, Italy
| | - A Rambaldi
- Department of Hematology and Oncology, Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy; School of Medicine, University of Milan, Milan, Italy
| | - P L Zinzani
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), Bologna University School of Medicine, Bologna, Italy
| | - B Casadei
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), Bologna University School of Medicine, Bologna, Italy
| | - E Derenzini
- Onco-Hematology Unit, European Institute of Oncology, IRCCS, Milan, Italy
| | - G Loseto
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - A Pileri
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), Bologna University School of Medicine, Bologna, Italy
| | - V Tabanelli
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan, Italy
| | - S Fiori
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan, Italy
| | - A Rivas-Delgado
- CIBERONC, Barcelona, Spain; Hematology Department, Hospital Clínic, Barcelona, Spain; IDIBAPS, Barcelona, Spain
| | - A López-Guillermo
- CIBERONC, Barcelona, Spain; Hematology Department, Hospital Clínic, Barcelona, Spain; IDIBAPS, Barcelona, Spain
| | - T Venesio
- Pathology Department, Candiolo Cancer Institute, Turin, Italy
| | - A Sapino
- Pathology Department, Candiolo Cancer Institute, Turin, Italy
| | - E Campo
- CIBERONC, Barcelona, Spain; Haematopathology Unit, Pathology Department, Hospital Clínic, Barcelona, Spain; University of Barcelona, Barcelona, Spain
| | - C Tripodo
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - A Guarini
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - S A Pileri
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan, Italy.
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17
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Olivero M, Erriquez J, Arigoni M, Capellero S, D'Ambrosio C, Mittica G, Borella F, Katsaros D, Privitera S, Berrino E, Venesio T, Valabrega G, Calogero R, Renzo MFD. Abstract GMM-023: PATIENT DERIVED XENOGRAFTS (PDXS) AND PDX DERIVED TUMOR CELLS (PDTC) ALLOW THE IDENTIFICATION OF ACTIONABLE CANCER GENES AND TREATMENT OPTIONS FOR PLATINUM REFRACTORY/RESISTANT OVARIAN CARCINOMAS. Clin Cancer Res 2019. [DOI: 10.1158/1557-3265.ovcasymp18-gmm-023] [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
Patients with advanced ovarian cancers have experienced little improvement in overall survival with standard treatments even after the incorporation of anti-angiogenic therapies. Besides anti-PARP inhibitors, matching individual critical genomic alterations with the best available drugs has not advanced as in other cancers, likely because a handful of cancer-related genes are mutated at high frequency, while many more are found mutated at much lower frequencies. This so called “mutation tail” is not only long but also mostly unexplored.
We used Patient Derived Xenografts (PDXs) to identify actionable cancer genes and PDX Derived Tumor Cells (PDTCs) to accelerate the discovery of treatment options. We envisioned that the alleged weakness of PDX models, i.e. lack of human stromal and immune cells, might be instrumental to identify mutations in cancer and to test approved or experimental targeted drugs as monotherapy or in different combinations to link biomarkers to treatments.
Forty-nine PDX lines from metastatic epithelial ovarian carcinomas have been propagated and fully characterized as far as histology, immunohistochemistry of epithelial and high-grade serous-specific markers and presence of TP53 and BRCA1/2 mutations.
Copy number variations (CNV) analysis and Whole Exome Sequencing (WES) were carried out PDX lines derived from naïve metastatic high-grade epithelial ovarian carcinomas, which came out to be refractory/resistant to platinum drugs. We studied non-synonymous mutations with allele frequencies ≥0.1. Only mutations in cancer genes listed in databases were further analyzed. SNPdb allowed ruling out polymorphisms. SIFT and PROVEAN softwares predicted deleterious or damaging effects onto the protein sequences. DGIdb helped selecting actionable genes.
We identified in one PDX line, a possibly loss-of-function mutation of the PIK3R1 gene (encoding the p85alpha regulatory subunit of PI3K) had an allele frequency=0.9 in early and late passages. Moreover, in two micro-dissected FFPE samples of the source tumor this mutation had an allele frequency nearly identical to that of the mutated TP53. Hence, PIK3R1W624R could be a trunk mutation in the PDX line and possibly in the human counterpart.
Treatment options were assayed ex-vivo, on short-term cultures of PDTCs of the PIK3R1W624R PDX line. Buparlisib, a pan-class I PI3K inhibitor, showed the ability to block proliferation of PDTCs and the growth in vivo of PDXs in regression preclinical trial. These data proofed-the-concept that a PDX-based pipeline is able to unveil actionable pathways for the treatment of advanced/metastatic ovarian cancer.
Citation Format: Martina Olivero, Jessica Erriquez, Maddalena Arigoni, Sonia Capellero, Concetta D'Ambrosio, Gloria Mittica, Fulvio Borella, Dionyssios Katsaros, Silvana Privitera, Enrico Berrino, Tiziana Venesio, Giorgio Valabrega, Raffaele Calogero and Maria Flavia Di Renzo. PATIENT DERIVED XENOGRAFTS (PDXS) AND PDX DERIVED TUMOR CELLS (PDTC) ALLOW THE IDENTIFICATION OF ACTIONABLE CANCER GENES AND TREATMENT OPTIONS FOR PLATINUM REFRACTORY/RESISTANT OVARIAN CARCINOMAS [abstract]. In: Proceedings of the 12th Biennial Ovarian Cancer Research Symposium; Sep 13-15, 2018; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2019;25(22 Suppl):Abstract nr GMM-023.
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Affiliation(s)
- Martina Olivero
- 1Department of Oncology, University of Torino, Torino, Italy,
- 2Candiolo Cancer Institute FPO-IRCCS, Candiolo (Torino) Italy,
| | | | | | - Sonia Capellero
- 1Department of Oncology, University of Torino, Torino, Italy,
- 2Candiolo Cancer Institute FPO-IRCCS, Candiolo (Torino) Italy,
| | - Concetta D'Ambrosio
- 1Department of Oncology, University of Torino, Torino, Italy,
- 2Candiolo Cancer Institute FPO-IRCCS, Candiolo (Torino) Italy,
| | - Gloria Mittica
- 2Candiolo Cancer Institute FPO-IRCCS, Candiolo (Torino) Italy,
| | - Fulvio Borella
- 4AOU Citta' della Salute, S.Anna Hospital, Torino, Italy
| | | | | | - Enrico Berrino
- 2Candiolo Cancer Institute FPO-IRCCS, Candiolo (Torino) Italy,
| | - Tiziana Venesio
- 2Candiolo Cancer Institute FPO-IRCCS, Candiolo (Torino) Italy,
| | - Giorgio Valabrega
- 1Department of Oncology, University of Torino, Torino, Italy,
- 2Candiolo Cancer Institute FPO-IRCCS, Candiolo (Torino) Italy,
| | | | - Maria Flavia Di Renzo
- 1Department of Oncology, University of Torino, Torino, Italy,
- 2Candiolo Cancer Institute FPO-IRCCS, Candiolo (Torino) Italy,
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18
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Zhang X, Garnerone S, Simonetti M, Harbers L, Nicoś M, Mirzazadeh R, Venesio T, Sapino A, Hartman J, Marchiò C, Bienko M, Crosetto N. CUTseq is a versatile method for preparing multiplexed DNA sequencing libraries from low-input samples. Nat Commun 2019; 10:4732. [PMID: 31628304 PMCID: PMC6802095 DOI: 10.1038/s41467-019-12570-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 09/17/2019] [Indexed: 12/14/2022] Open
Abstract
Current multiplexing strategies for massively parallel sequencing of genomic DNA mainly rely on library indexing in the final steps of library preparation. This procedure is costly and time-consuming, because a library must be generated separately for each sample. Furthermore, library preparation is challenging in the case of fixed samples, such as DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissues. Here we describe CUTseq, a method that uses restriction enzymes and in vitro transcription to barcode and amplify genomic DNA prior to library construction. We thoroughly assess the sensitivity and reproducibility of CUTseq in both cell lines and FFPE samples, and demonstrate an application of CUTseq for multi-region DNA copy number profiling within single FFPE tumor sections, to assess intratumor genetic heterogeneity at high spatial resolution. In conclusion, CUTseq is a versatile and cost-effective method for library preparation for reduced representation genome sequencing, which can find numerous applications in research and diagnostics. Genomics DNA library preparation from formalin-fixed paraffin-embedded tissues is challenging. Here the authors describe CUTseq that uses restriction enzymes and in vitro amplification to barcode samples for reduced representation genome sequencing.
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Affiliation(s)
- Xiaolu Zhang
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17165, Sweden
| | - Silvano Garnerone
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17165, Sweden
| | - Michele Simonetti
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17165, Sweden
| | - Luuk Harbers
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17165, Sweden
| | - Marcin Nicoś
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17165, Sweden.,Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20954, Lublin, Poland
| | - Reza Mirzazadeh
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17165, Sweden
| | - Tiziana Venesio
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo (TO), Italy
| | - Anna Sapino
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo (TO), Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, SE-17177, Sweden.,Department of Clinical Pathology, Karolinska University Laboratory, 17176, Stockholm, Sweden
| | - Caterina Marchiò
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo (TO), Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Magda Bienko
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17165, Sweden.
| | - Nicola Crosetto
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17165, Sweden.
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19
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Corso S, Isella C, Bellomo SE, Apicella M, Durando S, Migliore C, Ughetto S, D'Errico L, Menegon S, Moya-Rull D, Cargnelutti M, Capelôa T, Conticelli D, Giordano J, Venesio T, Balsamo A, Marchiò C, Degiuli M, Reddavid R, Fumagalli U, De Pascale S, Sgroi G, Rausa E, Baiocchi GL, Molfino S, Pietrantonio F, Morano F, Siena S, Sartore-Bianchi A, Bencivenga M, Mengardo V, Rosati R, Marrelli D, Morgagni P, Rausei S, Pallabazzer G, De Simone M, Ribero D, Marsoni S, Sottile A, Medico E, Cassoni P, Sapino A, Pectasides E, Thorner AR, Nag A, Drinan SD, Wollison BM, Bass AJ, Giordano S. A Comprehensive PDX Gastric Cancer Collection Captures Cancer Cell-Intrinsic Transcriptional MSI Traits. Cancer Res 2019; 79:5884-5896. [PMID: 31585941 DOI: 10.1158/0008-5472.can-19-1166] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/05/2019] [Accepted: 09/25/2019] [Indexed: 11/16/2022]
Abstract
Gastric cancer is the world's third leading cause of cancer mortality. In spite of significant therapeutic improvements, the clinical outcome for patients with advanced gastric cancer is poor; thus, the identification and validation of novel targets is extremely important from a clinical point of view. We generated a wide, multilevel platform of gastric cancer models, comprising 100 patient-derived xenografts (PDX), primary cell lines, and organoids. Samples were classified according to their histology, microsatellite stability, Epstein-Barr virus status, and molecular profile. This PDX platform is the widest in an academic institution, and it includes all the gastric cancer histologic and molecular types identified by The Cancer Genome Atlas. PDX histopathologic features were consistent with those of patients' primary tumors and were maintained throughout passages in mice. Factors modulating grafting rate were histology, TNM stage, copy number gain of tyrosine kinases/KRAS genes, and microsatellite stability status. PDX and PDX-derived cells/organoids demonstrated potential usefulness to study targeted therapy response. Finally, PDX transcriptomic analysis identified a cancer cell-intrinsic microsatellite instability (MSI) signature, which was efficiently exported to gastric cancer, allowing the identification, among microsatellite stable (MSS) patients, of a subset of MSI-like tumors with common molecular aspects and significant better prognosis. In conclusion, we generated a wide gastric cancer PDX platform, whose exploitation will help identify and validate novel "druggable" targets and optimize therapeutic strategies. Moreover, transcriptomic analysis of gastric cancer PDXs allowed the identification of a cancer cell-intrinsic MSI signature, recognizing a subset of MSS patients with MSI transcriptional traits, endowed with better prognosis. SIGNIFICANCE: This study reports a multilevel platform of gastric cancer PDXs and identifies a MSI gastric signature that could contribute to the advancement of precision medicine in gastric cancer.
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Affiliation(s)
- Simona Corso
- Department of Oncology, University of Torino, Candiolo, Italy. .,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | | | | | | | | | - Cristina Migliore
- Department of Oncology, University of Torino, Candiolo, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Stefano Ughetto
- Department of Oncology, University of Torino, Candiolo, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Laura D'Errico
- Department of Oncology, University of Torino, Candiolo, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | | | - Daniel Moya-Rull
- Department of Oncology, University of Torino, Candiolo, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | | | - Tânia Capelôa
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Daniela Conticelli
- Department of Oncology, University of Torino, Candiolo, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Jessica Giordano
- Department of Oncology, University of Torino, Candiolo, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | | | | | - Caterina Marchiò
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Torino, Italy
| | | | | | | | | | - Giovanni Sgroi
- Surgical Oncology Unit, Surgical Science Department, ASST Bergamo Ovest, Treviglio (BG), Italy
| | - Emanuele Rausa
- Surgical Oncology Unit, Surgical Science Department, ASST Bergamo Ovest, Treviglio (BG), Italy
| | - Gian Luca Baiocchi
- Department of Clinical and Experimental Sciences, Surgical Clinic, University of Brescia, Italy
| | - Sarah Molfino
- Department of Clinical and Experimental Sciences, Surgical Clinic, University of Brescia, Italy
| | - Filippo Pietrantonio
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Federica Morano
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Salvatore Siena
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy.,Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Andrea Sartore-Bianchi
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy.,Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Maria Bencivenga
- First Department of General Surgery, Borgo Trento Hospital, University of Verona, Verona, Italy
| | - Valentina Mengardo
- First Department of General Surgery, Borgo Trento Hospital, University of Verona, Verona, Italy
| | - Riccardo Rosati
- Gastroenterological Surgery Unit, IRCCS San Raffaele Hospital, Vita-Salute University, Milan, Italy
| | - Daniele Marrelli
- Department of Medicine, Surgery and Neurosciences, Unit of General Surgery and Surgical Oncology, University of Siena, Siena, Italy
| | - Paolo Morgagni
- Pathology Unit, Morgagni-Pierantoni Hospital, Forlì, Italy
| | - Stefano Rausei
- Department of Surgery, University of Insubria, Varese, Italy
| | | | | | - Dario Ribero
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | | | | | - Enzo Medico
- Department of Oncology, University of Torino, Candiolo, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Paola Cassoni
- Department of Medical Sciences, University of Torino, Italy
| | - Anna Sapino
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Torino, Italy
| | - Eirini Pectasides
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Aaron R Thorner
- Center for Cancer Genome Discovery (CCGD) Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Anwesha Nag
- Center for Cancer Genome Discovery (CCGD) Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Samantha D Drinan
- Center for Cancer Genome Discovery (CCGD) Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Bruce M Wollison
- Center for Cancer Genome Discovery (CCGD) Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Adam J Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Silvia Giordano
- Department of Oncology, University of Torino, Candiolo, Italy. .,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
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20
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Siravegna G, Mussolin B, Venesio T, Marsoni S, Seoane J, Dive C, Papadopoulos N, Kopetz S, Corcoran RB, Siu LL, Bardelli A. How liquid biopsies can change clinical practice in oncology. Ann Oncol 2019; 30:1580-1590. [PMID: 31373349 DOI: 10.1093/annonc/mdz227] [Citation(s) in RCA: 202] [Impact Index Per Article: 40.4] [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] [Indexed: 12/24/2022] Open
Abstract
Cell-free DNA fragments are shed into the bloodstream by tumor cells. The analysis of circulating tumor DNA (ctDNA), commonly known as liquid biopsy, can be exploited for a variety of clinical applications. ctDNA is being used to genotype solid cancers non-invasively, to track tumor dynamics and to detect the emergence of drug resistance. In a few settings, liquid biopsies have already entered clinical practice. For example, ctDNA is used to guide treatment in a subset of lung cancers. In this review, we discuss how recent improvements in the sensitivity and accuracy of ctDNA analyses have led to unprecedented advances in this research field. We further consider what is required for the routine deployment of liquid biopsies in the clinical diagnostic space. We pinpoint technical hurdles that liquid biopsies have yet to overcome, including preanalytical and analytical challenges. We foresee how liquid biopsies will transform clinical practice: by complementing (or replacing) imaging to monitor treatment response and by detecting minimal residual disease after surgery with curative intent.
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Affiliation(s)
- G Siravegna
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy; Department of Oncology, University of Torino, Candiolo, Turin, Italy
| | - B Mussolin
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - T Venesio
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - S Marsoni
- IFOM, Istituto FIRC di Oncología Molecolare, Milan, Italy
| | - J Seoane
- Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital and Universitat Autonoma de Barcelona, CIBERONC, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - C Dive
- Clinical and Experimental Pharmacology Group and Manchester Centre for Cancer Biomarker Sciences, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - N Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, USA; Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | - S Kopetz
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R B Corcoran
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, USA
| | - L L Siu
- Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
| | - A Bardelli
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy; Department of Oncology, University of Torino, Candiolo, Turin, Italy.
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21
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Scatolini M, Grosso E, Mello-Grand M, Ostano P, Coppo R, Patel A, Vitiello M, Venesio T, Zaccagna A, Pisacane A, Sarotto I, Taverna D, Poliseno L, Chiorino G, Bergamaschi D. 476 GJB5 association with BRAF mutation and survival in cutaneous melanoma. J Invest Dermatol 2019. [DOI: 10.1016/j.jid.2019.07.526] [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: 11/15/2022]
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22
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Berrino E, Miglio U, Miano V, Lanzetti L, Benvenuti S, Debernardi C, Bortoli MID, Marchio C, Venesio T, Sapino A. Abstract 261: L1- MET transcription silencing modulates MET and EGFR gene and their protein expression and induces apoptosis and cell-death in different types of cancer cells. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-261] [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
The activation of the LINE-1 sequence located within the second intron of MET leads to the onset of L1-MET transcript. We recently characterized the full L1-MET structure in breast cancer and showed that high levels of this transcript recognize a subset of more aggressive breast carcinomas, mainly of triple negative phenotype. However, at present, the relationship between L1-MET and MET is still poorly understood. In order to elucidate this function, we silenced L1-MET transcription using cells expressing different levels of L1-MET/MET, including lung cancer (A549 and EBC1), gastric cancer (GTL16), and breast cancer (MDA-MB231), that were transiently transfected with Gapmers-LNA (Exiqon), specifically targeting L1-MET sequence. Cell viability and apoptosis were evaluated after 24 h by cell count, Cell Titer Glow (Promega) and propidium iodide/annexin based-cytofluorimeter assays. RNA was purified from sample and control cells to assess the L1-METsilencing by qRT-PCR and to evaluate the gene-expression of a subset of cancer-related genes using Nanostring Technology, whereas western blot analyses were carried out to measure the protein expressions. A significant decrease of cell viability was detected in A549, EBC1 and GTL16, but not in MDA-MB231 cells, characterized by the lowest level of L1-MET overall. In parallel, the highly expressing L1-MET cells showed an increased rate of early and late apoptosis together with a strong reduction of MET gene and its protein expression. On the contrary, in MDA-MB231 cells L1-MET silencing induced only a slight MET gene and protein impairment. Overall, L1-MET knock-down caused a decrease expression of a conserved gene cluster, including a marked reduction of EGFR protein expression. Moreover, L1-MET silenced cells showed lower MET and EGFR phosphorylation, with a downstream silencing effect on pERK and pAKT. Results of cell treatment with the inhibitors of lysosome and proteasome activity bafilomycin and MG-132 ruled out the interaction of L1-MET silencing with protein degradation pathway. This is the first study investigating the function of the L1-MET transcript in cancer models. Our results show that although L1-MET is unable to encode for a protein, its silencing exerts a strong phenotypic effect on different tumor cell types, suggesting potential regulations at the transcriptional level.
Note: This abstract was not presented at the meeting.
Citation Format: Enrico Berrino, Umberto Miglio, Valentina Miano, Letizia Lanzetti, Silvia Benvenuti, Carla Debernardi, MIchele De Bortoli, Caterina Marchio, Tiziana Venesio, Anna Sapino. L1-MET transcription silencing modulates MET and EGFR gene and their protein expression and induces apoptosis and cell-death in different types of cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 261.
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Affiliation(s)
- Enrico Berrino
- 1University of Turin, FPO-IRCCS Candiolo Cancer Institute, Turin, Italy
| | | | | | | | | | | | | | - Caterina Marchio
- 1University of Turin, FPO-IRCCS Candiolo Cancer Institute, Turin, Italy
| | | | - Anna Sapino
- 1University of Turin, FPO-IRCCS Candiolo Cancer Institute, Turin, Italy
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Chiabotto G, Centomo ML, Merlini A, D'Ambrosio L, Sangiolo D, Miglio U, Todorovic M, Napione L, Berrino E, Capozzi F, Venesio T, Maldi E, Sapino A, Aglietta M, Grignani G, Pignochino Y. Antitumor activity of pazopanib (P) and trametinib (T) in preclinical models of osteosarcoma (OS). J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e22509] [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: 11/20/2022] Open
Abstract
e22509 Background: Receptor tyrosine kinases (RTKs) and their signal transducers are suitable targets for the treatment of advanced OS. We evaluated the antitumor activity of the RTK inhibitor P and the MEK inhibitor T and deeply investigated molecular mechanisms behind their activity and potential escape. Methods: Flow cytometry and western blot analyses were carried out in 7 OS cell lines to study the expression of RTK P targets and the activation of their pathways, respectively. Cell viability and colony growth were evaluated after 72h and 7-day treatment respectively, with scalar doses of both single agents and their constant combination. Cell cycle distribution and apoptosis were evaluated by flow cytometry after 72h. In vivo antitumor activity was studied in NOD/SCID mice bearing MNNG-HOS xenografts after 3 weeks of treatment. Cell migration was studied by scratch assays. The involvement of MAPK-PI3K pathway key transducers was explored by Vantage 3D RNA Panel and Nanostring technology, validated by western blot and confirmed by silencing experiments. Results: P targets are expressed on OS cell lines and their pathways are activated. P+T have synergistic antitumor activity (combination index < 1) in OS cell lines by inducing apoptosis (6/7) and inhibiting both ERK1/2(7/7) and AKT (7/7). Furthermore, in vivo antitumor activity was shown in OS bearing mice (tumor volume: P+T/untreated = 0.036, p = 0.002). P+T significantly down-modulated RTK EphaA2 (mean log2 fold change RNA P+T/untreated = -2.02±0.50) and induced Janus kinase MEK6 (mean log2 fold change RNA P+T/untreated = 2.9±0.51). EphA2 silencing reduced cellular proliferation and migration of OS cells. Impeding MEK6-up-regulation in P+T treated cells significantly increased the antitumor effect (51.5±14.3%) of the studied drugs. Conclusions: P+T exert antitumor activity in OS preclinical models through ERK and AKT inhibition and EphA2 downmodulation. MEK6-upregulation after P+T is likely implied in escape mechanism.
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Affiliation(s)
- Giulia Chiabotto
- Sarcoma Unit, Division of Medical Oncology, Candiolo Cancer Institute - FPO, IRCCS, Candiolo (To), Italy
| | - Maria Laura Centomo
- Sarcoma Unit, Division of Medical Oncology, Candiolo Cancer Institute - FPO, IRCCS, Candiolo (To), Italy
| | - Alessandra Merlini
- Sarcoma Unit, Division of Medical Oncology, Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Italy
| | - Lorenzo D'Ambrosio
- Sarcoma Unit, Division of Medical Oncology, Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Italy
| | - Dario Sangiolo
- Department of oncology, University of Torino Medical School, Torino, Italy
| | - Umberto Miglio
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo (To), Italy
| | - Maja Todorovic
- Institute for Cancer Research and Treatment at Candiolo, Candiolo, Italy
| | - Lucia Napione
- Department of Applied Science and Technology, Politecnico di Torino, Torino, Italy, Torino, Italy
| | - Enrico Berrino
- Dept. Medical Sciences, University of Turin, Torino, Italy
| | - Federica Capozzi
- Sarcoma Unit, Division of Medical Oncology, Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Italy
| | | | - Elena Maldi
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo (To), Italy
| | - Anna Sapino
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - Massimo Aglietta
- Division of Medical Oncology, Candiolo Cance rInstitute, FPO-IRCCS, Candiolo, Italy
| | - Giovanni Grignani
- Sarcoma Unit, Division of Medical Oncology, Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Italy
| | - Ymera Pignochino
- Sarcoma Unit, Division of Medical Oncology, Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Italy
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Molineris I, Levati L, Berrino E, D'Atri S, Menin C, Madonna G, Bulgarelli J, Ghiorzo P, Ferraresi V, Venesio T, Rivoltini L, Rodolfo M, Lanfrancone L, Mazzarella L, Guida A, Pelicci PG, De Maria R, Ascierto PA, Medico E, Russo G. The ACC melanoma pilot project: “Real-world” evaluation of an NGS platform for molecular characterization of melanoma in Italy. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e14600] [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: 11/20/2022] Open
Abstract
e14600 Background: Alliance Against Cancer (ACC), the network of Italian Cancer Centers, is involved in designing targeted NGS panels to enable sequencing a significant number of therapeutically actionable genes from FFPE tissue samples at the cost of a routine molecular diagnostic test (RMT). In this retrospective study we used the ACC oncochip v.1 on a cohort of stage III-IV metastatic melanoma patients, with the aim of: a) validating the diagnostic use of this oncochip in comparison with RMTs for BRAF mutation detection; b) evaluating how many additional actionable gene mutations can be identified per patient; c) evaluating possible associations between mutational profiles and outcome. Methods: DNA was extracted from 120 FFPE samples from 9 Italian hospitals previously profiled for BRAF status with a RMT, and matching germline samples. 60% of the patients underwent immunotherapy and 40% targeted therapy, with an overall survival ranging from few days to several years. 10-20 ng of DNA were profiled with the amplicon-based ACC Oncochip v.1, that covers ~700 Kb, including the full coding sequence of 182 genes. Samples were sequenced in a Ion Torrent S5 instrument (ThermoFisher), and mutational profiles were generated with the Ion Reporter software. Results: Adequate coverage of the BRAF codon 600 hotspot was reached in 99% of the samples, and BRAF status was 95% concordant with previous RMTs. In 4/6 discordant cases, BRAF V600 mutations were only detected by NGS (with VAF below 10%); in the remaining two cases NGS did not confirm mutations detected by RMT, possibly due to tumor heterogeneity. In accordance with TCGA data, BRAF was mutated in 55% of patients, NRAS in 23% and NF1 in 13%, with almost complete mutual exclusivity; moreover 86% of triple negative patients showed mutations in other actionable genes. We also observed great variability in mutational load, ranging from ~3 to > 500 somatic mutations per Mb; correlation between mutational profiles and clinical outcome is underway. Conclusions: The ACC Oncochip v.1 NGS panel is accurate and affordable, providing a comprehensive mutational profile for the cost of a RMT and allowing a precision medicine approach to melanoma diagnosis and identification of actionable mutations.
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Affiliation(s)
| | | | - Enrico Berrino
- Dept. Medical Sciences, University of Turin, Torino, Italy
| | | | - Chiara Menin
- 'Veneto Institute of Oncology'-IOV-IRCCS, Padova, Italy
| | - Gabriele Madonna
- Istituto Nazionale Tumori Fondazione Pascale-IRCCS, Napoli, Italy
| | - Jenny Bulgarelli
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola (FC), Italy
| | - Paola Ghiorzo
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | | | - Licia Rivoltini
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Monica Rodolfo
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | | | | | | | | | | | - Enzo Medico
- Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
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Varamo C, Peraldo-Neia C, Ostano P, Basiricò M, Raggi C, Bernabei P, Venesio T, Berrino E, Aglietta M, Leone F, Cavalloni G. Establishment and Characterization of a New Intrahepatic Cholangiocarcinoma Cell Line Resistant to Gemcitabine. Cancers (Basel) 2019; 11:cancers11040519. [PMID: 30979003 PMCID: PMC6520787 DOI: 10.3390/cancers11040519] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/05/2019] [Accepted: 04/07/2019] [Indexed: 12/19/2022] Open
Abstract
Intrahepatic cholangiocarcinoma (ICC) is one of the most lethal liver cancers. Late diagnosis and chemotherapy resistance contribute to the scarce outfit and poor survival. Resistance mechanisms are still poorly understood. Here, we established a Gemcitabine (GEM) resistant model, the MT-CHC01R1.5 cell line, obtained by a GEM gradual exposure (up to 1.5 µM) of the sensitive counterpart, MT-CHC01. GEM resistance was irreversible, even at high doses. The in vitro and in vivo growth was slower than MT-CHC01, and no differences were highlighted in terms of migration and invasion. Drug prediction analysis suggested that Paclitaxel and Doxycycline might overcome GEM resistance. Indeed, in vitro MT-CHC01R1.5 growth was reduced by Paclitaxel and Doxycycline. Importantly, Doxycycline pretreatment at very low doses restored GEM sensitivity. To assess molecular mechanisms underlying the acquisition of GEM resistance, a detailed analysis of the transcriptome in MT-CHC01R1.5 cells versus the corresponding parental counterpart was performed. Transcriptomic analysis showed that most up-regulated genes were involved in cell cycle regulation and in the DNA related process, while most down-regulated genes were involved in the response to stimuli, xenobiotic metabolism, and angiogenesis. Furthermore, additional panels of drug resistance and epithelial to mesenchymal transition genes (n = 168) were tested by qRT-PCR and the expression of 20 genes was affected. Next, based on a comparison between qRT-PCR and microarray data, a list of up-regulated genes in MT-CHC01R1.5 was selected and further confirmed in a primary cell culture obtained from an ICC patient resistant to GEM. In conclusion, we characterized a new GEM resistance ICC model that could be exploited either to study alternative mechanisms of resistance or to explore new therapies.
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Affiliation(s)
- Chiara Varamo
- Department of Oncology, University of Turin, 10100 Torino, Italy.
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, Center for Cancer Biology, KU Leuven, B3000 Leuven, Belgium.
| | | | - Paola Ostano
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, 13900 Biella, Italy.
| | - Marco Basiricò
- Division of Medical Oncology, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Torino, Italy.
| | - Chiara Raggi
- Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, 20089 Rozzano, Italy.
- Dept. Medicina Sperimentale e Clinica, Università di Firenze, 50100 Florence, Italy.
| | - Paola Bernabei
- Flow Cytometry Center, Candiolo Cancer Institute FPO-IRCCS, 10060 Candiolo, Torino, Italy.
| | - Tiziana Venesio
- Molecular Pathology Lab, Unit of Pathology, Candiolo Cancer Institute FPO-IRCCS, 10060 Candiolo, Torino, Italy.
| | - Enrico Berrino
- Molecular Pathology Lab, Unit of Pathology, Candiolo Cancer Institute FPO-IRCCS, 10060 Candiolo, Torino, Italy.
- Department of Medical Sciences, University of Turin, Corso Dogliotti 14, 10126 Turin, Italy.
| | - Massimo Aglietta
- Department of Oncology, University of Turin, 10100 Torino, Italy.
- Division of Medical Oncology, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Torino, Italy.
| | - Francesco Leone
- Department of Oncology, University of Turin, 10100 Torino, Italy.
- Division of Medical Oncology, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Torino, Italy.
| | - Giuliana Cavalloni
- Division of Medical Oncology, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Torino, Italy.
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Miglio U, Berrino E, Panero M, Ferrero G, Coscujuela Tarrero L, Miano V, Dell'Aglio C, Sarotto I, Annaratone L, Marchiò C, Comoglio PM, De Bortoli M, Pasini B, Venesio T, Sapino A. The expression of LINE1-MET chimeric transcript identifies a subgroup of aggressive breast cancers. Int J Cancer 2018; 143:2838-2848. [PMID: 30144023 DOI: 10.1002/ijc.31831] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 07/17/2018] [Accepted: 08/15/2018] [Indexed: 01/03/2023]
Abstract
Demethylation of the long interspersed nuclear element (LINE-1; L1) antisense promoter can result in transcription of neighboring sequences as for the L1-MET transcript produced by the L1 placed in the second intron of MET. To define the role of L1-MET, we investigated the sequence and the transcription of L1-MET in vitro models and heterogeneous breast cancers, previously reported to show other L1-derived transcripts. L1-MET expressing cell lines were initially identified in silico and investigated for L1-MET promoter methylation, cDNA sequence and cell fraction mRNA. The transcriptional level of L1-MET and MET were then evaluated in breast specimens, including 9 cancer cell lines, 41 carcinomas of different subtypes, and 11 normal tissues. In addition to a L1-MET transcript ending at MET exon 21, six novel L1-MET splice variants were identified. Normal breast tissues were negative for the L1-MET expression, whereas the triple-negative breast cancer (TNBC) and the high-grade carcinomas were enriched with the L1-MET mRNA (p = 0.005 and p = 0.018, respectively). In cancer cells and tissues the L1-MET expression was associated with its promoter hypomethylation (ρ = -0.8 and -0.9, respectively). No correlation was found between L1-MET and MET mRNA although L1-MET expressing tumors with higher L1-MET/MET ratio were negative for the MET protein expression (p = 0.006). Besides providing the first identification and detailed description of L1-MET in breast cancer, we clearly demonstrate that higher levels of this transcript specifically recognize a subset of more aggressive carcinomas, mainly TNBC. We suggest the possible evaluation of L1-MET in the challenging diagnosis of early TNBCs.
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Affiliation(s)
- Umberto Miglio
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Enrico Berrino
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Mara Panero
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Giulio Ferrero
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, Italy.,Department of Computer Science, University of Turin, Turin, Italy
| | | | - Valentina Miano
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, Italy
| | - Carmine Dell'Aglio
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Ivana Sarotto
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Laura Annaratone
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Caterina Marchiò
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Paolo M Comoglio
- Molecular Therapeutics and Exploratory Research Laboratory, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Michele De Bortoli
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, Italy
| | - Barbara Pasini
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Tiziana Venesio
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Anna Sapino
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
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Olivero M, Erriquez J, Arigoni M, Capellero S, D'Ambrosio C, Mittica G, Borella F, Katsaros D, Privitera S, Berrino E, Venesio T, Valabrega G, Calogero R, Renzo MFD. Abstract 3102: Identification of actionable cancer genes and treatment options for metastatic ovarian carcinomas using patient-derived xenografts and PDX-derived tumor cells. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3102] [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
Patients with advanced ovarian cancers have experienced little improvement in overall survival with standard treatments even after the incorporation of anti-angiogenic therapies. Besides anti-PARP inhibitors, matching individual critical genomic alterations with the best available drugs has not advanced as in other cancers, likely because a handful of cancer-related genes are mutated at high frequency, while many more are found mutated at much lower frequencies. This so called “mutation tail” is not only long but also mostly unexplored.
We used Patient Derived Xenografts (PDXs) to identify actionable cancer genes and PDX Derived Tumor Cells (PDTCs) to accelerate the discovery of treatment options. We envisioned that the alleged weakness of PDX models, i.e. lack of human stromal and immune cells, might be instrumental to identify mutations in cancer and to test approved or experimental targeted drugs as monotherapy or in different combinations to link biomarkers to treatments.
Fourty-nine PDX lines from metastatic epithelial ovarian carcinomas have been propagated and fully characterized as far as histology, immunohistochemistry of epithelial and high-grade serous-specific markers and presence of TP53 and BRCA1/2 mutations.
Copy number variations (CNV) analysis and Whole Exome Sequencing (WES) were carried out of 12 PDX lines derived from naïve metastatic high-grade serous epithelial ovarian carcinomas. We studied non-synonymous mutations with allele frequencies ≥0.1. Only mutations in cancer genes listed in databases were further analyzed. SNPdb allowed ruling out polymorphisms. SIFT and PROVEAN softwares predicted deleterious or damaging effects onto the protein sequences. DGIdb helped selecting actionable genes.
We identified mutations in 1-4 cancer genes in 8/12 PDX lines. In one PDX line, a possibly loss-of-function mutation of the PIK3R1 gene (encoding the p85alpha regulatory subunit of PI3K) had an allele frequency=0.9 in early and late passages. Moreover, in two micro-dissected FFPE samples of the source tumor this mutation had an allele frequency nearly identical to that of the mutated TP53. Hence, PIK3R1W624R could be a trunk mutation in the PDX line and possibly in the human counterpart.
Treatment options were assayed ex-vivo, on short-term cultures of PDTCs of the PIK3R1W624R PDX line. Buparlisib, a pan-class I PI3K inhibitor, showed the ability to block proliferation of PDTCs and the growth in vivo of PDXs in regression preclinical trial. These data proofed-the-concept that a PDX-based pipeline is able to unveil actionable pathways for the treatment of advanced/metastatic ovarian cancer.
Citation Format: Martina Olivero, Jessica Erriquez, Maddalena Arigoni, Sonia Capellero, Concetta D'Ambrosio, Gloria Mittica, Fulvio Borella, Dionyssios Katsaros, Silvana Privitera, Enrico Berrino, Tiziana Venesio, Giorgio Valabrega, Raffaele Calogero, Maria Flavia Di Renzo. Identification of actionable cancer genes and treatment options for metastatic ovarian carcinomas using patient-derived xenografts and PDX-derived tumor cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3102.
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Affiliation(s)
- Martina Olivero
- 1Candiolo Cancer Institute FPO-IRCCS, Univ. of Torino, Candiolo (Torino), Italy
| | | | | | - Sonia Capellero
- 1Candiolo Cancer Institute FPO-IRCCS, Univ. of Torino, Candiolo (Torino), Italy
| | - Concetta D'Ambrosio
- 1Candiolo Cancer Institute FPO-IRCCS, Univ. of Torino, Candiolo (Torino), Italy
| | - Gloria Mittica
- 1Candiolo Cancer Institute FPO-IRCCS, Univ. of Torino, Candiolo (Torino), Italy
| | - Fulvio Borella
- 4AOU Città della Salute, S.Anna Hospital, University of Torino, Torino, Italy
| | - Dionyssios Katsaros
- 4AOU Città della Salute, S.Anna Hospital, University of Torino, Torino, Italy
| | - Silvana Privitera
- 4AOU Città della Salute, S.Anna Hospital, University of Torino, Torino, Italy
| | - Enrico Berrino
- 2Candiolo Cancer Institute FPO-IRCCS, Candiolo (Torino), Italy
| | - Tiziana Venesio
- 2Candiolo Cancer Institute FPO-IRCCS, Candiolo (Torino), Italy
| | - Giorgio Valabrega
- 1Candiolo Cancer Institute FPO-IRCCS, Univ. of Torino, Candiolo (Torino), Italy
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Errichiello E, Venesio T. Author Correction: Mitochondrial DNA variants in colorectal carcinogenesis: Drivers or passengers? J Cancer Res Clin Oncol 2018; 144:1399. [PMID: 29721666 DOI: 10.1007/s00432-018-2650-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The affiliation detail for the corresponding author, Edoardo Errichiello, was published incorrectly. The correct detail read as follows.
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Affiliation(s)
- Edoardo Errichiello
- Department of Molecular Medicine, University of Pavia, Via Forlanini 14, 27100, Pavia, Italy.
| | - Tiziana Venesio
- Molecular Pathology Laboratory, Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Starda Provinciale 142, Candiolo, 10060, Turin, Italy
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Bussolati G, Annaratone L, Berrino E, Miglio U, Panero M, Cupo M, Gugliotta P, Venesio T, Sapino A, Marchiò C. Acid-free glyoxal as a substitute of formalin for structural and molecular preservation in tissue samples. PLoS One 2017; 12:e0182965. [PMID: 28796828 PMCID: PMC5552132 DOI: 10.1371/journal.pone.0182965] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/27/2017] [Indexed: 11/24/2022] Open
Abstract
Tissue fixation in phosphate buffered formalin (PBF) remains the standard procedure in histopathology, since it results in an optimal structural, antigenic and molecular preservation that justifies the pivotal role presently played by diagnoses on PBF-fixed tissues in precision medicine. However, toxicity of formaldehyde causes an environmental concern and may demand substitution of this reagent. Having observed that the reported drawbacks of commercially available glyoxal substitutes of PBF (Prefer, Glyo-fix, Histo-Fix, Histo-CHOICE, and Safe-Fix II) are likely related to their acidity, we have devised a neutral fixative, obtained by removing acids from the dialdehyde glyoxal with an ion-exchange resin. The resulting glyoxal acid-free (GAF) fixative has been tested in a cohort of 30 specimens including colon (N = 25) and stomach (N = 5) cancers. Our results show that GAF fixation produces a tissue and cellular preservation similar to that produced by PBF. Comparable immuno-histochemical and molecular (DNA and RNA) analytical data were obtained. We observed a significant enrichment of longer DNA fragment size in GAF-fixed compared to PBF-fixed samples. Adoption of GAF as a non-toxic histological fixative of choice would require a process of validation, but the present data suggest that it represents a reliable candidate.
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Affiliation(s)
- Gianni Bussolati
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Laura Annaratone
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Enrico Berrino
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), IRCCS, Candiolo, Italy
| | - Umberto Miglio
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), IRCCS, Candiolo, Italy
| | - Mara Panero
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), IRCCS, Candiolo, Italy
| | - Marco Cupo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Tiziana Venesio
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), IRCCS, Candiolo, Italy
| | - Anna Sapino
- Department of Medical Sciences, University of Turin, Turin, Italy
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), IRCCS, Candiolo, Italy
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin, Turin, Italy
- Pathology Division, Azienda Ospedaliera Universitaria Città della Salute e della Scienza di Torino, Turin, Italy
- * E-mail:
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Venesio T, Siravegna G, Bardelli A, Sapino A. Liquid Biopsies for Monitoring Temporal Genomic Heterogeneity in Breast and Colon Cancers. Pathobiology 2017; 85:146-154. [PMID: 28614831 DOI: 10.1159/000473882] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/31/2017] [Indexed: 11/19/2022] Open
Abstract
Cancer is a spatial and temporal dynamic disease where differently evolving genetic clones are responsible for progression. In this landscape, the genomic heterogeneity of the primary tumours can be captured by deep-sequencing representative spatial samples. However, the recognition of genetic alterations responsible for tumour evolution remains a challenging task. Recently, the "liquid biopsy" was recognized as a powerful real-time approach for the molecular monitoring of this dynamic disease. The term "liquid biopsy" generally refers to the use of circulating (cell-free) tumour DNA (ctDNA) and circulating tumour cells (CTCs) as non-invasive biomarkers for the early diagnosis, prognosis, monitoring of clinical progression, and response to treatment in different types of tumours, including the highly genomic heterogeneous breast cancer. The implementation and standardization of both approaches are still needed to achieve the required sensitivity and specificity to successfully analyze heterogenous tumours, but pivotal studies, in particular those concerning colorectal cancer, have shown the feasibility and usefulness of liquid biopsy for monitoring the Darwinian clonal evolution from an early to a metastatic stage.
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D'Ambrosio L, Palesandro E, Boccone P, Tolomeo F, Miano S, Galizia D, Manca A, Chiara G, Bertotto I, Russo F, Campanella D, Venesio T, Sangiolo D, Pignochino Y, Siatis D, De Simone M, Ferrero A, Pisacane A, Dei Tos AP, Aliberti S, Aglietta M, Grignani G. Impact of a risk-based follow-up in patients affected by gastrointestinal stromal tumour. Eur J Cancer 2017; 78:122-132. [PMID: 28448856 DOI: 10.1016/j.ejca.2017.03.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/16/2017] [Accepted: 03/24/2017] [Indexed: 12/18/2022]
Abstract
BACKGROUND Follow-up aims to precociously identify recurrences, metastases or treatment-related adverse events so as to undertake the appropriate therapy. Guidelines admit lack of knowledge on optimal surveillance schedule, but suggest follow-up based on experts' opinion and risk stratification. To identify the impact, if any, of regular follow-up, we interrogated our prospectively collected database whether early detection of recurrences affected both clinical management and, likely, the outcome. PATIENTS AND METHODS We required information to be available on primary surgery and ≥3°years of follow-up for non-recurring patients. We analysed recurrence characteristics (asymptomatic versus symptomatic, low- versus high tumour burden) and computed tomography (CT) scan counts to detect one recurrence. Kaplan-Meier method estimated recurrence-free survival (RFS), post-recurrence progression-free survival (PR-PFS), and disease-specific overall survival (OS). Comparisons used Hazard ratios (HR) with 95% confidence intervals (CIs). Multivariate analyses employed the Cox proportional hazards model. All tests were two-sided. RESULTS Between 01/2001 and 12/2012 we found 233 study-eligible patients. Estimated 5- and 10-year RFS were 61.8% and 50.4%, respectively. After a 68-month median follow-up, we observed 94 (40.3%) recurrences [73/94 (77.7%) asymptomatic versus 21/94 (22.3%) symptomatic and 45/94 (47.9%) low- versus 49/94 (52.1%) high tumour burden]. Multivariate analysis revealed that symptomatic and high tumour burden recurrences were highly predictive of both worse PR-PFS (HR:3.19, P < 0.001; HR:2.80, P = 0.003, respectively) and OS (HR:3.65, P < 0.001; HR:2.38, P = 0.026, respectively). Finally, 29 second (primary) cancers were detected during follow-up. CONCLUSIONS Regular follow-up detects recurrences at an earlier stage and may be associated with a better PR-PFS and OS for these patients. In the absence of randomised trials, these evidences support follow-up effort and cost.
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Affiliation(s)
- Lorenzo D'Ambrosio
- Sarcoma Unit, Division of Medical Oncology Candiolo Cancer Institute - FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, TO, Italy; University of Torino, Department of Oncology, Regione Gonzole, 10, 10043 Orbassano, TO, Italy
| | - Erica Palesandro
- Sarcoma Unit, Division of Medical Oncology Candiolo Cancer Institute - FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, TO, Italy; University of Torino, Department of Oncology, Regione Gonzole, 10, 10043 Orbassano, TO, Italy
| | - Paola Boccone
- Sarcoma Unit, Division of Medical Oncology Candiolo Cancer Institute - FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, TO, Italy; University of Torino, Department of Oncology, Regione Gonzole, 10, 10043 Orbassano, TO, Italy
| | - Francesco Tolomeo
- Sarcoma Unit, Division of Medical Oncology Candiolo Cancer Institute - FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, TO, Italy; University of Torino, Department of Oncology, Regione Gonzole, 10, 10043 Orbassano, TO, Italy
| | - Sara Miano
- Sarcoma Unit, Division of Medical Oncology Candiolo Cancer Institute - FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, TO, Italy; University of Torino, Department of Oncology, Regione Gonzole, 10, 10043 Orbassano, TO, Italy
| | - Danilo Galizia
- Sarcoma Unit, Division of Medical Oncology Candiolo Cancer Institute - FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, TO, Italy; University of Torino, Department of Oncology, Regione Gonzole, 10, 10043 Orbassano, TO, Italy
| | - Antonio Manca
- Radiology Unit, Candiolo Cancer Institute - FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, TO, Italy
| | - Gabriele Chiara
- Radiology Unit, Candiolo Cancer Institute - FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, TO, Italy
| | - Ilaria Bertotto
- Radiology Unit, Candiolo Cancer Institute - FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, TO, Italy
| | - Filippo Russo
- Radiology Unit, Candiolo Cancer Institute - FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, TO, Italy
| | - Delia Campanella
- Radiology Unit, Candiolo Cancer Institute - FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, TO, Italy
| | - Tiziana Venesio
- Pathology Unit, Candiolo Cancer Institute - FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, TO, Italy
| | - Dario Sangiolo
- Sarcoma Unit, Division of Medical Oncology Candiolo Cancer Institute - FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, TO, Italy; University of Torino, Department of Oncology, Regione Gonzole, 10, 10043 Orbassano, TO, Italy
| | - Ymera Pignochino
- Sarcoma Unit, Division of Medical Oncology Candiolo Cancer Institute - FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, TO, Italy; University of Torino, Department of Oncology, Regione Gonzole, 10, 10043 Orbassano, TO, Italy
| | - Dimitrios Siatis
- Surgical Oncology Unit, Candiolo Cancer Institute - FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, TO, Italy
| | - Michele De Simone
- Surgical Oncology Unit, Candiolo Cancer Institute - FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, TO, Italy
| | - Alessandro Ferrero
- Department of General and Oncological Surgery, Ospedale Mauriziano "Umberto I", Via Magellano 1, 10128 Torino, TO, Italy
| | - Alberto Pisacane
- Pathology Unit, Candiolo Cancer Institute - FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, TO, Italy
| | - Angelo Paolo Dei Tos
- Department of Pathology and Molecular Genetics, Treviso General Hospital, Piazza Ospedale 23, 31100 Treviso, TV, Italy; University of Padova, Department of Medicine, Via 8 febbraio 2, 35122 Padova, PD, Italy
| | - Sandra Aliberti
- Sarcoma Unit, Division of Medical Oncology Candiolo Cancer Institute - FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, TO, Italy
| | - Massimo Aglietta
- Sarcoma Unit, Division of Medical Oncology Candiolo Cancer Institute - FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, TO, Italy; University of Torino, Department of Oncology, Regione Gonzole, 10, 10043 Orbassano, TO, Italy
| | - Giovanni Grignani
- Sarcoma Unit, Division of Medical Oncology Candiolo Cancer Institute - FPO, IRCCS, Strada Provinciale 142, Km 3.95, 10060 Candiolo, TO, Italy; University of Torino, Department of Oncology, Regione Gonzole, 10, 10043 Orbassano, TO, Italy.
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Errichiello E, Venesio T. Mitochondrial DNA variants in colorectal carcinogenesis: Drivers or passengers? J Cancer Res Clin Oncol 2017; 143:1905-1914. [PMID: 28393270 DOI: 10.1007/s00432-017-2418-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/03/2017] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Mitochondrial DNA alterations have widely been reported in many age-related degenerative diseases and tumors, including colorectal cancer. In the past few years, the discovery of inter-genomic crosstalk between nucleus and mitochondria has reinforced the role of mitochondrial DNA variants in perturbing this essential signaling pathway and thus indirectly targeting nuclear genes involved in tumorigenic and invasive phenotype. FINDINGS Mitochondrial dysfunction is currently considered a crucial hallmark of carcinogenesis as well as a promising target for anticancer therapy. Mitochondrial DNA alterations include point mutations, deletions, inversions, and copy number variations, but numerous studies investigating their pathogenic role in cancer have provided inconsistent evidence. Furthermore, the biological impact of mitochondrial DNA variants may vary tremendously, depending on the proportion of mutant DNA molecules carried by the neoplastic cells (heteroplasmy). CONCLUSIONS In this review, we discuss the role of different type of mitochondrial DNA alterations in colorectal carcinogenesis and, in particular, we revisit the issue of whether they may be considered as causative driver or simply genuine passenger events. The advent of high-throughput techniques as well as the development of genetic and pharmaceutical interventions for the treatment of mitochondrial dysfunction in colorectal cancer are also explored.
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Affiliation(s)
- Edoardo Errichiello
- Department of Molecular Medicine, University of Pavia, Via Forlanini 14, 27100, Pavia, Italy.
- Molecular Pathology Laboratory, Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Starda Provinciale 142, Candiolo, 10060, Turin, Italy.
| | - Tiziana Venesio
- Molecular Pathology Laboratory, Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Starda Provinciale 142, Candiolo, 10060, Turin, Italy
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Furlan D, Trapani D, Berrino E, Debernardi C, Panero M, Libera L, Sahnane N, Riva C, Tibiletti MG, Sessa F, Sapino A, Venesio T. Oxidative DNA damage induces hypomethylation in a compromised base excision repair colorectal tumourigenesis. Br J Cancer 2017; 116:793-801. [PMID: 28141798 PMCID: PMC5355935 DOI: 10.1038/bjc.2017.9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 10/28/2016] [Revised: 12/23/2016] [Accepted: 01/05/2017] [Indexed: 12/12/2022] Open
Abstract
Background: A compromised base excision repair (BER) promotes carcinogenesis by accumulating oxidative DNA-damaged products as observed in MUTYH-associated polyposis, a hereditary colorectal cancer syndrome marked by adenomas and cancers with an accumulation of 8-oxoguanine. Remarkably, DNA global demethylation has been shown to be mediated by BER, suggesting a relevant interplay with early colorectal tumourigenesis. To check this hypothesis, we investigated a cohort of 49 adenomas and 10 carcinomas, derived from 17 MUTYH-associated polyposis patients; as adenoma controls, we used a set of 36 familial adenomatous polyposis and 24 sporadic polyps. Methods: Samples were analysed for their mutational and epigenetic status, measured as global LINE-1 (long interspersed nuclear element) and gene-specific LINE-1 MET methylation by mass spectrometry and pyrosequencing. Results: MUTYH-associated polyposis adenomas were strikingly more hypomethylated than familial adenomatous and sporadic polyps for both DNA demethylation markers (P=0.032 and P=0.007 for LINE-1; P=0.004 and P<0.0001 for LINE-1 MET, respectively) with levels comparable to those of the carcinomas derived from the same patients. They also had mutations due mainly to KRAS/NRAS p.G12C, which was absent in the controls (P<0.0001 for both sets). Conclusions: Our results show that DNA demethylation, together with specific KRAS/NRAS mutations, drives the early steps of oxidative damage colorectal tumourigenesis.
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Affiliation(s)
- Daniela Furlan
- Anatomic Pathology Unit, Department of Surgical and Morphological Sciences, University of Insubria, Varese 21100, Italy.,Research Center for the Study of Hereditary and Familial Tumors, University of Insubria, Varese 21100, Italy
| | - Davide Trapani
- Anatomic Pathology Unit, Department of Surgical and Morphological Sciences, University of Insubria, Varese 21100, Italy
| | - Enrico Berrino
- Molecular Pathology Laboratory, Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Strada Provinciale 142, Candiolo (Torino) 10060, Italy
| | - Carla Debernardi
- Molecular Pathology Laboratory, Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Strada Provinciale 142, Candiolo (Torino) 10060, Italy
| | - Mara Panero
- Molecular Pathology Laboratory, Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Strada Provinciale 142, Candiolo (Torino) 10060, Italy
| | - Laura Libera
- Anatomic Pathology Unit, Department of Surgical and Morphological Sciences, University of Insubria, Varese 21100, Italy
| | - Nora Sahnane
- Anatomic Pathology Unit, Department of Surgical and Morphological Sciences, University of Insubria, Varese 21100, Italy
| | - Cristina Riva
- Anatomic Pathology Unit, Department of Surgical and Morphological Sciences, University of Insubria, Varese 21100, Italy.,Research Center for the Study of Hereditary and Familial Tumors, University of Insubria, Varese 21100, Italy
| | - Maria Grazia Tibiletti
- Anatomic Pathology Unit, Department of Surgical and Morphological Sciences, University of Insubria, Varese 21100, Italy
| | - Fausto Sessa
- Anatomic Pathology Unit, Department of Surgical and Morphological Sciences, University of Insubria, Varese 21100, Italy.,Research Center for the Study of Hereditary and Familial Tumors, University of Insubria, Varese 21100, Italy
| | - Anna Sapino
- Molecular Pathology Laboratory, Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Strada Provinciale 142, Candiolo (Torino) 10060, Italy
| | - Tiziana Venesio
- Molecular Pathology Laboratory, Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Strada Provinciale 142, Candiolo (Torino) 10060, Italy
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Marabelli M, Molinaro V, Abou Khouzam R, Berrino E, Panero M, Balsamo A, Venesio T, Ranzani GN. Colorectal Adenomatous Polyposis: Heterogeneity of Susceptibility Gene Mutations and Phenotypes in a Cohort of Italian Patients. Genet Test Mol Biomarkers 2016; 20:777-785. [PMID: 27705013 DOI: 10.1089/gtmb.2016.0198] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 12/20/2022] Open
Abstract
AIMS Colorectal adenomatous polyposis entailing cancer predisposition is caused by constitutional mutations in different genes. APC is associated with the familial adenomatous polyposis (FAP/AFAP) and MUTYH with the MUTYH-associated polyposis (MAP), while POLE and POLD1 mutations cause the polymerase proofreading-associated polyposis (PPAP). METHODS We screened for mutations in patients with multiple adenomas/FAP: 121 patients were analyzed for APC and MUTYH mutations, and 36 patients were also evaluated for POLE and POLD1 gene mutations. RESULTS We found 20 FAP/AFAP, 15 MAP, and no PPAP subjects: pathogenic mutations proved to be heterogeneous, and included 5 APC and 1 MUTYH novel mutations. The mutation detection rate was significantly different between patients with 5-100 polyps and those with >100 polyps (p = 8.154 × 10-7), with APC mutations being associated with an aggressive phenotype (p = 1.279 × 10-9). Mean age at diagnosis was lower in FAP/AFAP compared to MAP (p = 3.055 × 10-4). Mutation-negative probands showed a mean age at diagnosis that was significantly higher than FAP/AFAP (p = 3.46986 × 10-7) and included 45.3% of patients with <30 polyps and 70.9% of patients with no family history. CONCLUSIONS This study enlarges the APC and MUTYH mutational spectra, and also evaluated variants of uncertain significance, including the MUTYH p.Gln338His mutation. Moreover this study underscores the phenotypic heterogeneity and genotype-phenotype correlations in a cohort of Italian patients.
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Affiliation(s)
- Monica Marabelli
- 1 Department of Biology and Biotechnology, University of Pavia , Pavia, Italy
| | - Valeria Molinaro
- 1 Department of Biology and Biotechnology, University of Pavia , Pavia, Italy
| | - Raefa Abou Khouzam
- 1 Department of Biology and Biotechnology, University of Pavia , Pavia, Italy
| | | | - Mara Panero
- 2 Candiolo Cancer Institute , FPO-IRCCS, Torino, Italy
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Laface R, Venesio T, Cagnazzo C, Pollato K, Cicako T, Aglietta M, Garetto L. Rare epidermal growth factor receptor (EGFR) mutations in a 425 patients population with non-small cell lung cancer (NSCLC): clinical, molecular and survival data. The IRCCS Candiolo experience. Ann Oncol 2015. [DOI: 10.1093/annonc/mdv343.15] [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: 11/12/2022] Open
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Errichiello E, Balsamo A, Cerni M, Venesio T. Mitochondrial variants in MT-CO2 and D-loop instability are involved in MUTYH-associated polyposis. J Mol Med (Berl) 2015; 93:1271-81. [PMID: 26138249 DOI: 10.1007/s00109-015-1312-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [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: 01/31/2015] [Revised: 05/28/2015] [Accepted: 06/16/2015] [Indexed: 12/21/2022]
Abstract
UNLABELLED Mitochondrial DNA alterations have been widely reported in different human tumours, including colorectal carcinoma, but their mutational spectrum and pathogenic role in specific subsets of patients with polyposis syndromes have been poorly investigated. We compared the breadth of somatic variants across the mitochondrial genome of MUTYH-associated polyposis (MAP) patients with homogeneous groups of classical/attenuated familial adenomatous polyposis (FAP/AFAP) and sporadic cases. Overall, we screened 121 adenomas and seven adenocarcinomas and their corresponding germinal controls, for mitochondrial genes with a crucial role in oxidative phosphorylation and translation (MT-CO1, MT-CO2, MT-CO3, MT-TD, MT-TS1, MT-ATP6) as well as a hypervariable sequence (HV-II) within the control region displacement loop (D-loop), a marker of hypermutability and clonal expansion. The sequencing analysis revealed the presence of 17 variants, mostly causing non-synonymous changes in conserved amino acid residues, typically distributed in the MT-CO2 gene of MAP patients (P < 0.0001), who frequently carried the hot spot m.7763G>A variant. Accordingly, D-loop instability was also significantly associated with variants grouped inside the MT-CO2 gene (P = 0.0061). This is the first report showing a locus-specific distribution of mitochondrial DNA alterations in a subtype of colorectal tumourigenesis. In addition, our findings suggest that MT-CO2 variants, representing early molecular events in MAP tumorigenesis, might be a potential prognostic biomarker for the cancer-risk assessment of patients affected by this syndrome. KEY MESSAGES We compared the frequencies of mtDNA variants in MAP vs. FAP/AFAP/sporadic patients. We found a gene-specific (MT-CO2) distribution of mtDNA variants in MAP cases. Most mtDNA variants caused non-synonymous changes in conserved amino acid residues. D-loop instability was significantly associated with variants grouped inside MT-CO2. MT-CO2 variants might be a potential prognostic biomarker in MAP patients.
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Affiliation(s)
- Edoardo Errichiello
- Molecular Pathology Laboratory, Unit of Pathology, Institute for Cancer Research and Treatment, FPO-IRCCS, Strada Provinciale 142, 10060, Candiolo, Torino, Italy
| | - Antonella Balsamo
- Molecular Pathology Laboratory, Unit of Pathology, Institute for Cancer Research and Treatment, FPO-IRCCS, Strada Provinciale 142, 10060, Candiolo, Torino, Italy
| | - Marianna Cerni
- Molecular Pathology Laboratory, Unit of Pathology, Institute for Cancer Research and Treatment, FPO-IRCCS, Strada Provinciale 142, 10060, Candiolo, Torino, Italy
| | - Tiziana Venesio
- Molecular Pathology Laboratory, Unit of Pathology, Institute for Cancer Research and Treatment, FPO-IRCCS, Strada Provinciale 142, 10060, Candiolo, Torino, Italy.
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Barault L, Amatu A, Bleeker FE, Moutinho C, Falcomatà C, Fiano V, Cassingena A, Siravegna G, Milione M, Cassoni P, De Braud F, Rudà R, Soffietti R, Venesio T, Bardelli A, Wesseling P, de Witt Hamer P, Pietrantonio F, Siena S, Esteller M, Sartore-Bianchi A, Di Nicolantonio F. Digital PCR quantification of MGMT methylation refines prediction of clinical benefit from alkylating agents in glioblastoma and metastatic colorectal cancer. Ann Oncol 2015; 26:1994-1999. [PMID: 26113646 DOI: 10.1093/annonc/mdv272] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 06/11/2015] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND O(6)-methyl-guanine-methyl-transferase (MGMT) silencing by promoter methylation may identify cancer patients responding to the alkylating agents dacarbazine or temozolomide. PATIENTS AND METHODS We evaluated the prognostic and predictive value of MGMT methylation testing both in tumor and cell-free circulating DNA (cfDNA) from plasma samples using an ultra-sensitive two-step digital PCR technique (methyl-BEAMing). Results were compared with two established techniques, methylation-specific PCR (MSP) and Bs-pyrosequencing. RESULTS Thresholds for MGMT methylated status for each technique were established in a training set of 98 glioblastoma (GBM) patients. The prognostic and the predictive value of MGMT methylated status was validated in a second cohort of 66 GBM patients treated with temozolomide in which methyl-BEAMing displayed a better specificity than the other techniques. Cutoff values of MGMT methylation specific for metastatic colorectal cancer (mCRC) tissue samples were established in a cohort of 60 patients treated with dacarbazine. In mCRC, both quantitative assays methyl-BEAMing and Bs-pyrosequencing outperformed MSP, providing better prediction of treatment response and improvement in progression-free survival (PFS) (P < 0.001). Ability of methyl-BEAMing to identify responding patients was validated in a cohort of 23 mCRC patients treated with temozolomide and preselected for MGMT methylated status according to MSP. In mCRC patients treated with dacarbazine, exploratory analysis of cfDNA by methyl-BEAMing showed that MGMT methylation was associated with better response and improved median PFS (P = 0.008). CONCLUSIONS Methyl-BEAMing showed high reproducibility, specificity and sensitivity and was applicable to formalin-fixed paraffin-embedded tissues and cfDNA. This study supports the quantitative assessment of MGMT methylation for clinical purposes since it could refine prediction of response to alkylating agents.
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Affiliation(s)
- L Barault
- Experimental Clinical Molecular Oncology, Candiolo Cancer Institute-FPO, IRCCS, Candiolo (Turin)
| | - A Amatu
- Niguarda Cancer Center, Ospedale Niguarda Ca' Granda, Milan, Italy
| | - F E Bleeker
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - C Moutinho
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - C Falcomatà
- Experimental Clinical Molecular Oncology, Candiolo Cancer Institute-FPO, IRCCS, Candiolo (Turin)
| | - V Fiano
- Department of Medical Sciences, University of Turin, Città Della Salute e Della Scienza Hospital, Turin
| | - A Cassingena
- Niguarda Cancer Center, Ospedale Niguarda Ca' Granda, Milan, Italy
| | - G Siravegna
- Experimental Clinical Molecular Oncology, Candiolo Cancer Institute-FPO, IRCCS, Candiolo (Turin); Department of Oncology, University of Torino, Candiolo (Turin); FIRC Institute of Molecular Oncology (IFOM), Milan
| | - M Milione
- Departments of Pathology and Laboratory Medicine
| | - P Cassoni
- Department of Medical Sciences, University of Turin, Città Della Salute e Della Scienza Hospital, Turin
| | - F De Braud
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan
| | - R Rudà
- Department of Neuro-Oncology, University of Turin and Città Della Salute e Della Scienza Hospital, Turin, Italy
| | - R Soffietti
- Department of Neuro-Oncology, University of Turin and Città Della Salute e Della Scienza Hospital, Turin, Italy
| | - T Venesio
- Experimental Clinical Molecular Oncology, Candiolo Cancer Institute-FPO, IRCCS, Candiolo (Turin)
| | - A Bardelli
- Experimental Clinical Molecular Oncology, Candiolo Cancer Institute-FPO, IRCCS, Candiolo (Turin); Department of Oncology, University of Torino, Candiolo (Turin)
| | - P Wesseling
- Department of Pathology, VU University Medical Center, Amsterdam; Department of Pathology, Radboud University Medical Center, Nijmegen
| | - P de Witt Hamer
- Department Neurosurgery, Neurosurgical Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | | | - S Siena
- Niguarda Cancer Center, Ospedale Niguarda Ca' Granda, Milan, Italy
| | - M Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain; Department of Physiological Sciences II, School of Medicine, University of Barcelona, Catalonia; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - F Di Nicolantonio
- Experimental Clinical Molecular Oncology, Candiolo Cancer Institute-FPO, IRCCS, Candiolo (Turin); Department of Oncology, University of Torino, Candiolo (Turin).
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Peraldo Neia C, Cavalloni G, Balsamo A, Venesio T, Napoli F, Sassi F, Martin V, Frattini M, Aglietta M, Leone F. Screening for the FIG-ROS1 fusion in biliary tract carcinomas by nested PCR. Genes Chromosomes Cancer 2014; 53:1033-40. [PMID: 25231053 DOI: 10.1002/gcc.22212] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 08/08/2014] [Indexed: 01/30/2023] Open
Abstract
ROS1 rearrangements have been detected in a variety of tumors and are considered as suitable targets of anticancer therapies. We developed a new, quick, specific, and sensitive PCR test to screen for the FIG-ROS1 fusion and applied it to a series of Italian patients with bile duct carcinoma (BTC). Formalin-fixed, paraffin-embedded tissues, derived from 65 Italian BTC patients, and six cell lines were analyzed by nested PCR to investigate the prevalence of a previously reported FIG-ROS1 fusion. The specificity and sensitivity of nested PCR were investigated in FIG-ROS1 positive U118MG cells in reconstitution experiments with peripheral blood mononuclear cells. We found that six out of 65 (9%) BTC patients were positive for the FIG-ROS1 fusion, comprising two out of 14 (14%) gallbladder carcinoma (GBC) patients and four out of 25 (16%) extrahepatic cholangiocarcinoma (ECC) patients. None of the 26 intrahepatic cholangiocarcinoma cases harbored the FIG-ROS1 fusion. All the cell lines were negative for this variant. In conclusion, 14-16% of GBC and ECC were positive for FIG-ROS1. This may have clinical implications, since these patients will potentially benefit from the treatment with specific ROS1 inhibitors.
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Affiliation(s)
- Caterina Peraldo Neia
- Department of Oncology, University of Turin Medical School, IRCCS-Candiolo, Turin, Italy
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Lucci-Cordisco E, Risio M, Venesio T, Genuardi M. The growing complexity of the intestinal polyposis syndromes. Am J Med Genet A 2013; 161A:2777-87. [PMID: 24124059 DOI: 10.1002/ajmg.a.36253] [Citation(s) in RCA: 36] [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] [Received: 08/01/2013] [Accepted: 09/05/2013] [Indexed: 12/12/2022]
Abstract
Familial adenomatous polyposis has been the first form of inherited intestinal polyposis to be recognized. For a long time it has been considered the main polyposis syndrome, associated with an easily recognizable phenotype, with a marginal role attributed to a few very rare hamartomatous conditions. More recently, it has been gradually demonstrated that the intestinal polyposes encompass a range of conditions within a wide spectrum of disease severity, polyp histology, and extraintestinal manifestations. A growing number of genes and phenotypes has been identified, and heterogeneity of somatic molecular pathways underlying epithelial transformation in different syndromes and associated tumors has been documented. Increasing knowledge on the molecular bases and more widespread use of genetic tests has shown phenotypic overlaps between conditions that were previously considered distinct, highlighting diagnostic difficulties. With the advent of next generation sequencing, the diagnosis and the classification of these syndromes will be progressively based more on genetic testing results. However, the phenotypic variability documented among patients with mutations in the same genes cannot be fully explained by different expressivity, indicating a role for as yet unknown modifying factors. Until the latter will be identified, the management of patients with polyposis syndromes should be guided by both clinical and genetic findings.
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Affiliation(s)
- Emanuela Lucci-Cordisco
- Institute of Medical Genetics, "A. Gemelli" School of Medicine, Catholic University, Rome, Italy
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Venesio T, Balsamo A, Errichiello E, Ranzani GN, Risio M. Oxidative DNA damage drives carcinogenesis in MUTYH-associated-polyposis by specific mutations of mitochondrial and MAPK genes. Mod Pathol 2013; 26:1371-81. [PMID: 23599153 DOI: 10.1038/modpathol.2013.66] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 01/28/2013] [Accepted: 01/28/2013] [Indexed: 12/29/2022]
Abstract
MUTYH is a DNA-base-excision-repair gene implicated in the activation of nuclear and mitochondrial cell-death pathways. MUTYH germline mutations cause an inherited polyposis, MUTYH-associated-polyposis, characterized by multiple adenomas and increased susceptibility to colorectal cancer. Since this carcinogenesis remains partially unknown, we searched for nuclear and mitochondrial gene alterations that may drive the tumorigenic process. Ninety-six adenomas and 7 carcinomas from 12 MUTYH-associated-polyposis and 13 classical/attenuated adenomatous polyposis patients were investigated by sequencing and pyrosequencing for the presence of mutations in KRAS, BRAF, MT-CO1/MT-CO2 and MT-TD genes. KRAS mutations were identified in 24% MUTYH-associated-polyposis vs 15% classical/attenuated familial polyposis adenomas; mutated MUTYH-associated-polyposis adenomas exhibited only c.34G>T transversions in codon 12, an alteration typically associated with oxidative DNA damage, or mutations in codon 13; neither of these mutations was found in classical/attenuated familial polyposis adenomas (P<0.001). Mutated MUTYH-associated-polyposis carcinomas showed KRAS c.34G>T transversions, prevalently occurring with BRAFV600E; none of the classical/attenuated familial polyposis carcinomas displayed these alterations. Comparing mitochondrial DNA from lymphocytes and adenomas of the same individuals, we detected variants in 82% MUTYH-associated-polyposis vs 38% classical/attenuated familial polyposis patients (P=0.040). MT-CO1/MT-CO2 missense mutations, which cause aminoacid changes, were only found in MUTYH-associated-polyposis lesions and were significantly associated with KRAS mutations (P=0.0085). We provide evidence that MUTYH-associated-polyposis carcinogenesis is characterized by the occurrence of specific mutations in both KRAS and phylogenetically conserved genes of mitochondrial DNA which are involved in controlling oxidative phosphorylation; this implies the existence of a colorectal tumorigenesis in which changes in mitochondrial functions cooperate with RAS-induced malignant transformation.
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Affiliation(s)
- Tiziana Venesio
- Unit of Pathology, Institute for Cancer Research and Treatment, Candiolo, (Torino), Italy
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Gammaitoni L, Giraudo L, Leuci V, Todorovic M, Mesiano G, Picciotto F, Pisacane A, Zaccagna A, Volpe MG, Gallo S, Caravelli D, Giacone E, Venesio T, Balsamo A, Pignochino Y, Grignani G, Carnevale-Schianca F, Aglietta M, Sangiolo D. Effective activity of cytokine-induced killer cells against autologous metastatic melanoma including cells with stemness features. Clin Cancer Res 2013; 19:4347-58. [PMID: 23794732 DOI: 10.1158/1078-0432.ccr-13-0061] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [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
PURPOSE We investigate the unknown tumor-killing activity of cytokine-induced killer (CIK) cells against autologous metastatic melanoma and the elusive subset of putative cancer stem cells (mCSC). EXPERIMENTAL DESIGN We developed a preclinical autologous model using same patient-generated CIK cells and tumor targets to consider the unique biology of each patient/tumor pairing. In primary tumor cell cultures, we visualized and immunophenotypically defined a putative mCSC subset using a novel gene transfer strategy that exploited their exclusive ability to activate the promoter of stemness gene Oct4. RESULTS The CIK cells from 10 patients with metastatic melanoma were successfully expanded (median, 23-fold; range, 11-117). Primary tumor cell cultures established and characterized from the same patients were used as autologous targets. Patient-derived CIK cells efficiently killed autologous metastatic melanoma [up to 71% specific killing (n = 26)]. CIK cells were active in vivo against autologous melanoma, resulting in delayed tumor growth, increased necrotic areas, and lymphocyte infiltration at tumor sites. The metastatic melanoma cultures presented an average of 11.5% ± 2.5% putative mCSCs, which was assessed by Oct4 promoter activity and stemness marker expression (Oct4, ABCG2, ALDH, MITF). Expression was confirmed on mCSC target molecules recognized by CIK cells (MIC A/B; ULBPs). CIK tumor killing activity against mCSCs was intense (up to 71%, n = 4) and comparable with results reported against differentiated metastatic melanoma cells (P = 0.8). CONCLUSIONS For the first time, the intense killing activity of CIK cells against autologous metastatic melanoma, including mCSCs, has been shown. These findings move clinical investigation of a new immunotherapy for metastatic melanoma, including mCSCs, closer.
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Affiliation(s)
- Loretta Gammaitoni
- Unit of Stem Cell Transplantation and Cell Therapy, Surgical Dermatology, Pathology, and Sarcoma, Fondazione del Piemonte per l'Oncologia, I.R.C.C.S.,Torino, Italy
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Palesandro E, Galizia D, D'Ambrosio L, Boccone P, Aliberti S, Venesio T, Manca A, Bertotto I, Chiara G, Russo F, Campanella D, Pignochino Y, Aglietta M, Grignani G. A risk-based individualized follow-up after complete surgery as an effective procedure to reduce the relapse (R) impact in GIST patients (pts). J Clin Oncol 2013. [DOI: 10.1200/jco.2013.31.15_suppl.10552] [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: 11/20/2022] Open
Abstract
10552 Background: FU care poses a burden on both pts and health system. FU aims to precociously identify recurrences, metastases or treatment-related adverse events so to undertake the appropriate therapy as soon as possible. Guidelines (NCCN, ESMO) admit lack of knowledge on optimal surveillance, but suggest FU based on experts’ opinion and risk stratification. Moreover, tumor burden (TB) is a well known negative prognostic factor (Van Glabbeke 2005). Therefore, low-TB at R might affect final outcome. To identify the impact, if any, of regular FU, we examined our prospectively collected database looking for Rs in which the early detection affected both clinical management and, likely, the outcome. Methods: 140 pts were stratified (AFIP classification). High risk (HR) pts had complete history + physical examination (H&P) and CT every 3 mos for 2 years, 4 mos in 3rd year, 6 mos in the 4th and 5th yrs, yearly thereafter; intermediate (IR), low (LR) and very low risk (VLR) pts had H&P + CT every 4 mos for 2 years, every 6 mos up to the 5th year, then yearly. Rs were divided in: low-TB + completely resectable R (Group 1) and high-TB + disseminated R (Group 2). The number of CT needed to detect (NND) one R and the incidence of early (<6 mos) R was calculated. Overall survival (OS) was estimated by Kaplan-Meier method. Results: In 73 male and 67 female, median age 63 (23-82), risk stratification was: HR 73, IR 31, LR 28, VLR 8. After a median FU of 63 mos we observed 58 Rs: 25 (43%) and 33 (57%) in group 2 and 1, respectively. Relapsed pts genotype was KIT Ex11 72%; Ex9 10%; Ex13 3%; wild-type 15%. Median time to R was 16 mos (1-120). 21 pts underwent surgical resection of their R. 16 pts remained free from progression for a median of 90 mos. We detected 15 (26%) early Rs. NND was 17 and 32 CT for HR and non-HR pts, respectively. Group 1 and 2 median estimated OS was 112 and 87 mos (p=.05), respectively. Conclusions: Though retrospective, this series shows that FU may detect low-TB Rs. In principle, this might affect pts final outcome and, therefore, justify this costly effort. Since it is difficult to foresee a prospective randomized trial, a confirmation of these data in a different series might increase their reliability.
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Affiliation(s)
- Erica Palesandro
- Medical Oncology, Institute for Cancer Research and Treatment, Candiolo, Italy
| | - Danilo Galizia
- Medical Oncology, Institute for Cancer Research and Treatment, Candiolo, Italy
| | - Lorenzo D'Ambrosio
- Medical Oncology, Institute for Cancer Research and Treatment, Candiolo, Italy
| | - Paola Boccone
- Medical Oncology, Institute for Cancer Research and Treatment, Candiolo, Italy
| | - Sandra Aliberti
- Medical Oncology, Institute for Cancer Research and Treatment, Candiolo, Italy
| | - Tiziana Venesio
- Unit of Pathology, Institute for Cancer Research and Treatment, Candiolo, Italy
| | - Antonio Manca
- Radiology Unit, Institute for Cancer Research and Treatment, Candiolo, Italy
| | - Ilaria Bertotto
- Radiology Unit, Institute for Cancer Research and Treatment, Candiolo, Italy
| | - Gabriele Chiara
- Radiology Unit, Institute for Cancer Research and Treatment, Candiolo, Italy
| | - Filippo Russo
- Radiology Unit, Institute for Cancer Research and Treatment, Candiolo, Italy
| | - Delia Campanella
- Radiology Unit, Institute for Cancer Research and Treatment, Candiolo, Italy
| | | | - Massimo Aglietta
- Medical Oncology, Institute for Cancer Research and Treatment, Candiolo, Italy
| | - Giovanni Grignani
- Medical Oncology, Institute for Cancer Research and Treatment, Candiolo, Italy
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Venesio T, Balsamo A, D'Agostino VG, Ranzani GN. MUTYH-associated polyposis (MAP), the syndrome implicating base excision repair in inherited predisposition to colorectal tumors. Front Oncol 2012; 2:83. [PMID: 22876359 PMCID: PMC3410368 DOI: 10.3389/fonc.2012.00083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [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: 05/11/2012] [Accepted: 07/16/2012] [Indexed: 12/24/2022] Open
Abstract
In 2002, Al-Tassan and co-workers described for the first time a recessive form of inherited polyposis associated with germline mutations of MUTYH, a gene encoding a base excision repair (BER) protein that counteracts the DNA damage induced by the oxidative stress. MUTYH-associated polyposis (MAP) is now a well-defined cancer susceptibility syndrome, showing peculiar molecular features that characterize disease progression. However, some aspects of MAP, including diagnostic criteria, genotype-phenotype correlations, pathogenicity of variants, as well as relationships between BER and other DNA repair pathways, are still poorly understood. A deeper knowledge of the MUTYH expression pattern is likely to refine our understanding of the protein role and, finally, to improve guidances for identifying and handling MAP patients.
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Affiliation(s)
- Tiziana Venesio
- Unit of Pathology, Institute for Cancer Research and Treatment Candiolo, Torino, Italy
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Risio M, Venesio T, Kolomoets E, Armaroli P, Gallo F, Balsamo A, Muto G, D'Urso L, Puppo P, Naselli A, Segnan N. Genetic polymorphisms of CYP17A1, vitamin D receptor and androgen receptor in Italian heredo-familial and sporadic prostate cancers. Cancer Epidemiol 2010; 35:e18-24. [PMID: 21094112 DOI: 10.1016/j.canep.2010.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Revised: 09/27/2010] [Accepted: 10/22/2010] [Indexed: 10/18/2022]
Abstract
BACKGROUND Searching for genetic and environmental factors predisposing to prostate cancer, common single-nucleotide polymorphisms in CYP17A1, CYP19A1, VDR genes, and the number of CAG repeats from AR were investigated in Italian heredo-familial prostate cancer (HFPC) patients controlled for dietary intake and life style habits. METHODS We evaluated differences between HFPC and sporadic cancers, in the pattern of common single-nucleotide polymorphisms in CYP17A1, CYP19A1, VDR genes, and the CAG repeat from AR, controlling for dietary intake and lifestyle habits in a regionwide population. Ninety-five patients with HFPC were identified and 378 sporadic prostate cancers were randomly selected as controls. Dietary intake and lifestyle habits were determined through self-administered questionnaires in all patients. Genotyping of polymorphisms for CYP17A1, CYP19A1, VDR, and the CAG repeat from AR was carried out using pyrosequencing. RESULTS HFPC cases were significantly younger than controls, whereas similar proportions of localized tumours, favourable histology, and abnormal prostate serum antigen levels (4-19 ng/ml) were detected in the two groups. A statistically evident gene-gene interaction was found: a 5-fold higher probability [odds ratio (OR)=4.83; 95% confidence interval (CI): 1.37-17.02] of HFPC was observed in the subgroup profiling VDR1 T/T genotypes coupled with VDR2 T/T genotype. Among nutrients, an increase in HFPC risk (OR=3.14; 95% CI: 1.12-8.81) was found only for zinc, when associated with the VDR2 T/T genotype. CONCLUSIONS Significant evidence for positive interactions between VDR1 and VDR2 genotypes was demonstrated, suggesting that high-risk multigenic polymorphism profiles could variously sustain HFPC tumorigenesis.
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Affiliation(s)
- Mauro Risio
- Unit of Pathology, Institute for Cancer Research and Treatment, Strada Provinciale 142, 10060 Candiolo (TO), Italy.
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Stella GM, Benvenuti S, Gramaglia D, Scarpa A, Tomezzoli A, Cassoni P, Senetta R, Venesio T, Pozzi E, Bardelli A, Comoglio PM. MET mutations in cancers of unknown primary origin (CUPs). Hum Mutat 2010; 32:44-50. [DOI: 10.1002/humu.21374] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 09/13/2010] [Indexed: 12/12/2022]
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Scatolini M, Grand MM, Grosso E, Venesio T, Pisacane A, Balsamo A, Sirovich R, Risio M, Chiorino G. Altered molecular pathways in melanocytic lesions. Int J Cancer 2010; 126:1869-1881. [PMID: 19795447 DOI: 10.1002/ijc.24899] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
To identify gene expression changes in melanocytic lesions, biopsies from 18 common nevi (CMN), 11 dysplastic nevi (DN), 8 radial and 15 vertical growth phase melanomas (RGPM, VGPM), and 5 melanoma metastases (MTS) were analyzed using whole genome microarrays. The comparison between CMN and RGPM showed an enrichment of Gene Ontology terms related to inter and intracellular junctions, whereas the transition from RGPM to VGPM underlined the alteration of apoptosis. Upregulation of genes involved in dsDNA break repair and downregulation of cellular adhesion genes were observed in MTS with respect to VGPM. DN exhibited rather heterogeneous molecular profiles, with some proliferation genes expressed at higher levels than in CMN, altered regulation of transcription compared to RGPM and a subset of processes, such as mismatch repair, equally expressed as in VGPM. Furthermore, the expression profile of genes involved into cellular detoxification and antigen presentation split them into two classes, with different proliferation potential. Finally, molecular profiling of individual lesions identified altered biological processes, such as regulation of apoptosis, regulation of transcription and T-cell activation, not associated with specific histological classes but rather with subgroups of samples without apparent relationship. This holds true for dysplastic nevi in particular. Our data indicate that generally the intersection between stage specific and sample specific molecular alterations may lead to a more precise determination of the individual progression risk of melanocytic lesions.
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Affiliation(s)
| | | | - Enrico Grosso
- Cancer Genomics Lab, Fondo Edo Tempia, Biella, Italy
| | - Tiziana Venesio
- Unit of Pathology, Institute for Cancer Research and Treatment (IRCC), Candiolo, Torino, Italy
| | - Alberto Pisacane
- Unit of Pathology, Institute for Cancer Research and Treatment (IRCC), Candiolo, Torino, Italy
| | - Antonella Balsamo
- Unit of Pathology, Institute for Cancer Research and Treatment (IRCC), Candiolo, Torino, Italy
| | | | - Mauro Risio
- Unit of Pathology, Institute for Cancer Research and Treatment (IRCC), Candiolo, Torino, Italy
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Pezzi A, Roncucci L, Benatti P, Sassatelli R, Varesco L, Di Gregorio C, Venesio T, Pedroni M, Maffei S, Reggiani Bonetti L, Borsi E, Ferrari M, Martella P, Rossi G, Ponz De Leon M. Relative role of APC and MUTYH mutations in the pathogenesis of familial adenomatous polyposis. Scand J Gastroenterol 2010; 44:1092-100. [PMID: 19593690 DOI: 10.1080/00365520903100481] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
OBJECTIVE Familial adenomatous polyposis (FAP) is an interesting model for the study of colorectal tumour. Two genes contribute to the FAP phenotype - APC and MUTYH - but their relative role is still undefined. The objective of this study was to evaluate the contribution of the two genes to the pathogenesis of FAP by means of a series of FAP families. MATERIAL AND METHODS Sixty-one unrelated families with a diagnosis of FAP and a total of 187 affected individuals were evaluated. After extracting DNA, APC and MUTYH genes were sequenced. RESULTS In the whole series of patients, colectomy with ileorectal anastomosis was the most frequent surgery, although the number of patients treated by total proctocolectomy and ileoanal anastomosis was increasing. Duodenal and jejunal-ileal adenomas were present in more than half of the patients. Constitutional mutations were detected in 37 of the 45 families (82.2%); there were 33 families with APC and 4 with MUTYH alterations. Age at onset of polyposis and age at surgery were 10-15 years delayed for carriers of MUTYH mutations; cancer at diagnosis was frequent, and extracolonic manifestations were diagnosed in the majority of MUTYH-positive families. MUTYH-associated polyposis showed the horizontal transmission expected for recessive inheritance (at variance with the dominant pattern seen with APC mutations). CONCLUSIONS At least two genes are associated with the FAP phenotype. APC mutations account for the majority of cases, while MUTYH mutations can be observed in 10% of patients. There are few but definite differences between APC- and MUTYH-associated FAP, such as age at diagnosis and pattern of transmission.
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Affiliation(s)
- Annalisa Pezzi
- Department of Internal Medicine, University of Modena and Reggio Emilia, Modena, Italy
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Casorzo L, Corigliano M, Ferrero P, Venesio T, Risio M. Evaluation of 7q31 region improves the accuracy of EGFR FISH assay in non small cell lung cancer. Diagn Pathol 2009; 4:36. [PMID: 19889201 PMCID: PMC2781797 DOI: 10.1186/1746-1596-4-36] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [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: 04/28/2009] [Accepted: 11/04/2009] [Indexed: 11/10/2022] Open
Abstract
Background Increase of EGFR gene copy number consequent to gene amplification and/or polysomy of chromosome 7 has been significantly associated with better clinical outcome in Non Small Cell Lung Cancer (NSCLC) patients treated with Tyrosin-Kinase Inhibitors (TKIs). The primary method to detect EGFR copy number is FISH (Fluorescence in Situ Hybridization), that in lung cancer requires a precise standardization due to the presence of intratumor heterogeneity and high frequency of chromosome 7 polysomy. Recommendations and interpretative guidelines to discriminate NSCLC patients into FISH positive (gene amplification and high chromosome 7 polysomy) and FISH negative have been proposed by the University of Colorado Cancer Center (UCCC). However, in a subset of cases the distinction between EGFR amplification and chromosome 7 polysomy can be controversial because of a complex pattern of multiple EGFR and centromere signals. Methods In order to distinguish more accurately these two genetic events, 20 NSCLC FISH positive patients, showing a controversial pattern of EGFR and centromere specific signals, were further evaluated for the status of 7q31 distal region. Results A discrepancy between FISH results obtained with UCCC scoring system and 7q31 control was evidenced in 2 patients (10%). Conclusion Our data strengthen the usefulness of 7q31 region evaluation to discriminate EGFR amplification from chromosome 7 polysomy in controversial EGFR FISH positive cases. Since it has been reported a possible different contribution of amplification and polysomy to TKIs susceptibility in NSCLC, the clear distinction between these two genetic events may be important to identify a subset of patients more responsive to the therapy.
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Affiliation(s)
- Laura Casorzo
- Unit of Pathology, Institute for Cancer Research and Treatment, Strada Provinciale 142, Candiolo-Torino, Italy.
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Ponti G, Losi L, Pellacani G, Wannesson L, Cesinaro A, Venesio T, Petti C, Seidenari S. Malignant melanoma in patients with hereditary nonpolyposis colorectal cancer. Br J Dermatol 2008; 159:162-8. [DOI: 10.1111/j.1365-2133.2008.08575.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Venesio T, Chiorino G, Balsamo A, Zaccagna A, Petti C, Scatolini M, Pisacane A, Sarotto I, Picciotto F, Risio M. In melanocytic lesions the fraction of BRAF V600E alleles is associated with sun exposure but unrelated to ERK phosphorylation. Mod Pathol 2008; 21:716-26. [PMID: 18408659 DOI: 10.1038/modpathol.2008.41] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BRAF(V600E) mutation has been frequently reported in different types of melanocytic lesions, but its role in melanomagenesis is poorly understood, having been associated with either the proliferative-induced MAPK pathway activation or the acquisition of oncogene-driven senescence. The presence of BRAF alterations has been related to sun exposure, although the molecular mechanisms underlying this event are only partly known. To elucidate the relationships among BRAF/NRAS alterations, MAPK pathway activation, and sun exposure, we examined 22 acquired nevi and 18 cutaneus melanomas from 38 patients. Microdissected tissues from each lesion were subjected to BRAF/NRAS mutation analysis by sequencing, allele-specific PCR and pyrosequencing assay. The same lesions were also examined for the expression of phosphorylated ERK1/2. Phototype and an accurate history of sun exposure were evaluated for each patient. BRAF(V600E) mutation was detected in 50% of the acquired nevi and in 70% of the cutaneus melanomas in the absence of NRAS alterations. The fraction of alleles carrying BRAF(V600E) substitution was variable but strongly associated with sun exposure. In contrast, no relationship was evidenced between the presence of this mutation and patients' phototype, phosphorylated ERK1/2 expression, or Clark's level. Our findings indicate that in melanocytic lesions, BRAF(V600E) mutation can affect a subset of the cells and is associated with the type and quantity of sun exposure. This mutation is independent of the nevo-melanoma progression and unrelated to ERK phosphorylation, suggesting that alternative mechanisms to the MAPK activation are also involved in this type of transformation.
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Affiliation(s)
- Tiziana Venesio
- Unit of Pathology, Institute for Cancer Research and Treatment, Candiolo, Torino, Italy.
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