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Laure A, Rigutto A, Kirschner MB, Opitz L, Grob L, Opitz I, Felley-Bosco E, Hiltbrunner S, Curioni-Fontecedro A. Genomic and Transcriptomic Analyses of Malignant Pleural Mesothelioma (MPM) Samples Reveal Crucial Insights for Preclinical Testing. Cancers (Basel) 2023; 15:2813. [PMID: 37345150 DOI: 10.3390/cancers15102813] [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: 04/19/2023] [Revised: 05/15/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023] Open
Abstract
Cell lines are extensively used to study cancer biology. However, the use of highly passaged commercial cell lines has to be questioned, as they do not closely resemble the originating tumor. To understand the reliability of preclinical models for Malignant pleural mesothelioma (MPM) studies, we have performed whole transcriptome and whole exome analyses of fresh frozen MPM tumors and compared them to cell lines generated from these tumors, as well as commercial cell lines and a preclinical MPM mouse model. Patient-derived cell lines were generated from digested fresh tumors and whole exome sequencing was performed on DNA isolated from formalin-fixed, paraffin-embedded (FFPE) tumor samples, corresponding patient-derived cell lines, and normal tissue. RNA sequencing libraries were prepared from 10 fresh frozen tumor samples, the 10 corresponding patient-derived cell lines, and 7 commercial cell lines. Our results identified alterations in tumor suppressor genes such as FBXW7, CDKN2A, CDKN2B, and MTAP, all known to drive MPM tumorigenesis. Patient-derived cell lines correlate to a high degree with their originating tumor. Gene expressions involved in multiple pathways such as EMT, apoptosis, myogenesis, and angiogenesis are upregulated in tumor samples when compared to patient-derived cell lines; however, they are downregulated in commercial cell lines compared to patient-derived cell lines, indicating significant differences between the two model systems. Our results show that the genome and transcriptome of tumors correlate to a higher degree with patient-derived cell lines rather than commercial cell lines. These results are of major relevance for the scientific community in regard to using cell lines as an appropriate model, resembling the pathway of interest to avoid misleading results for clinical applications.
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Affiliation(s)
- Alexander Laure
- Faculty of Science and Medicine, University of Fribourg, CH-1700 Fribourg, Switzerland
- Faculty of Science, University of Zurich, CH-8006 Zurich, Switzerland
| | - Angelica Rigutto
- Faculty of Science and Medicine, University of Fribourg, CH-1700 Fribourg, Switzerland
- Faculty of Science, University of Zurich, CH-8006 Zurich, Switzerland
| | - Michaela B Kirschner
- Department of Thoracic Surgery, University Hospital Zurich, CH-8091 Zurich, Switzerland
| | - Lennart Opitz
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology, University of Zurich, CH-8057 Zurich, Switzerland
| | - Linda Grob
- NEXUS Personalized Health Technologies, ETH Zurich, CH-8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Isabelle Opitz
- Faculty of Science, University of Zurich, CH-8006 Zurich, Switzerland
- Department of Thoracic Surgery, University Hospital Zurich, CH-8091 Zurich, Switzerland
| | - Emanuela Felley-Bosco
- Faculty of Science, University of Zurich, CH-8006 Zurich, Switzerland
- Laboratory of Molecular Oncology, Department of Thoracic Surgery, University Hospital Zurich, CH-8091 Zurich, Switzerland
| | - Stefanie Hiltbrunner
- Faculty of Science and Medicine, University of Fribourg, CH-1700 Fribourg, Switzerland
- Department of Medical Oncology and Haematology, University Hospital Zurich, CH-8091 Zurich, Switzerland
| | - Alessandra Curioni-Fontecedro
- Faculty of Science and Medicine, University of Fribourg, CH-1700 Fribourg, Switzerland
- Department of Medical Oncology and Haematology, University Hospital Zurich, CH-8091 Zurich, Switzerland
- Department of Oncology, HFR Fribourg-Hôpital Cantonal, CH-1708 Fribourg, Switzerland
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Laure A, Rigutto A, Manovah M, Chambon M, Turcatti G, Kirschner M, Opitz I, Hiltbrunner S, Curioni-Fontecedro A. 137P Repurposing drug screen of patient-derived malignant pleural mesothelioma cells reveals potential anti-cancer activity. J Thorac Oncol 2023. [DOI: 10.1016/s1556-0864(23)00392-1] [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: 04/03/2023]
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Laure A, Rigutto A, Kirschner M, Opitz L, Opitz I, Hiltbrunner S, Curioni-Fontecedro A. P1.14-01 Transcriptomic Analysis of Malignant Pleural Mesothelioma (MPM) Reveals Insights for Basic Research and Preclinical Testing. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.192] [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: 11/24/2022]
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Napoli F, Rapa I, Izzo S, Rigutto A, Libener R, Riganti C, Bironzo P, Taulli R, Papotti M, Volante M, Scagliotti G, Righi L. Correction to: Micro-RNA-215 and -375 regulate thymidylate synthase protein expression in pleural mesothelioma and mediate epithelial to mesenchymal transition. Virchows Arch 2022; 481:331. [PMID: 35670855 PMCID: PMC9343316 DOI: 10.1007/s00428-022-03355-y] [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: 11/30/2022]
Affiliation(s)
- Francesca Napoli
- Department of Oncology, University of Turin, San Luigi Hospital, Regione Gonzole 10, Orbassano, Turin, Italy
| | - Ida Rapa
- Pathology Unit, San Luigi Hospital, Orbassano, Turin, Italy
| | - Stefania Izzo
- Pathology Unit, San Luigi Hospital, Orbassano, Turin, Italy
| | - Angelica Rigutto
- Department of Oncology, University of Turin, San Luigi Hospital, Regione Gonzole 10, Orbassano, Turin, Italy.,Department of Medical Oncology and Hematology, University Hospital of Zurich, Zurich, Switzerland
| | - Roberta Libener
- Pathology Division, Saints Antonio and Biagio Hospital, Alessandria, Italy
| | - Chiara Riganti
- Department of Oncology, University of Turin, San Luigi Hospital, Regione Gonzole 10, Orbassano, Turin, Italy.,Interdepartmental Research Center of Molecular Biotechnology, University of Turin, Turin, Italy.,Interdepartmental Centre for Studies On Asbestos and Other Toxic Particulates, University of Turin, Turin, Italy
| | - Paolo Bironzo
- Department of Oncology, University of Turin, San Luigi Hospital, Regione Gonzole 10, Orbassano, Turin, Italy
| | - Riccardo Taulli
- Center for Experimental Research and Medical Studies (CeRMS), City of Health and Science University Hospital, Turin, Italy
| | - Mauro Papotti
- Department of Oncology, University of Turin, San Luigi Hospital, Regione Gonzole 10, Orbassano, Turin, Italy.,Pathology Unit, City of Health and Science University Hospital, Turin, Italy
| | - Marco Volante
- Department of Oncology, University of Turin, San Luigi Hospital, Regione Gonzole 10, Orbassano, Turin, Italy
| | - Giorgio Scagliotti
- Department of Oncology, University of Turin, San Luigi Hospital, Regione Gonzole 10, Orbassano, Turin, Italy
| | - Luisella Righi
- Department of Oncology, University of Turin, San Luigi Hospital, Regione Gonzole 10, Orbassano, Turin, Italy.
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Napoli F, Rapa I, Mortara U, Massa F, Izzo S, Rigutto A, Zambelli V, Bellevicine C, Troncone G, Papotti M, Volante M. MicroRNA profiling predicts positive nodal status in papillary thyroid carcinoma in the preoperative setting. Cancer Cytopathol 2022; 130:695-704. [PMID: 35500065 DOI: 10.1002/cncy.22585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/02/2022] [Accepted: 04/04/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND The molecular characterization of thyroid nodules in cytological samples has so far been focused on discriminating between benign and malignant forms in a purely diagnostic setting. The evidence on the impact of molecular biomarkers to determine the risk of aggressiveness in cytologically "neoplastic" lesions is limited to genomic alterations (such as BRAF and TERT mutations). The aim of our study was to assess the preoperative role of microRNAs (miRNAs) in predicting the nodal status of patients with papillary thyroid cancer. METHODS A pilot series of histological samples of papillary thyroid carcinoma with (6 cases) or without (6 cases) lymph node metastases, matched for other major clinical and pathological features, was analyzed for global miRNA expression in a screening phase. A set of miRNAs was then validated in a series of 63 consecutive cytological samples of papillary carcinomas: 48 pN-negative and 15 pN-positive at histology. RESULTS Unsupervised cluster analysis segregated surgical pN-negative and pN-positive samples, except for 1 case. The 45 differentially expressed miRNAs in pN-positive versus pN-negative cases were predicted to regulate a wide range of cellular pathways, enriched for Wnt, gonadotropin-releasing hormone receptor, and cerulein/cholecystokinin receptor signaling. In agreement with their profiles in surgical samples, 4 miRNAs of the 10 selected for validation (miR-154-3p, miR-299-5p, miR-376a-3p, and miR-302E) had a significant differential expression in cytological samples of papillary carcinoma with lymph node metastases and predicted the positive nodal status with a relatively good performance. CONCLUSIONS MiRNA profiling is a potential promising strategy to define papillary carcinoma aggressiveness in the preoperative setting.
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Affiliation(s)
- Francesca Napoli
- Department of Oncology, University of Turin, Orbassano, Turin, Italy
| | - Ida Rapa
- Pathology Unit, San Luigi Hospital, Turin, Italy
| | - Umberto Mortara
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | | | - Angelica Rigutto
- Department of Oncology, University of Turin, Orbassano, Turin, Italy.,Department of Medical Oncology and Hematology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Vanessa Zambelli
- Department of Oncology, University of Turin, Orbassano, Turin, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Mauro Papotti
- Department of Oncology, University of Turin, Orbassano, Turin, Italy
| | - Marco Volante
- Department of Oncology, University of Turin, Orbassano, Turin, Italy
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Hiltbrunner S, Mannarino L, Kirschner MB, Opitz I, Rigutto A, Laure A, Lia M, Nozza P, Maconi A, Marchini S, D’Incalci M, Curioni-Fontecedro A, Grosso F. Tumor Immune Microenvironment and Genetic Alterations in Mesothelioma. Front Oncol 2021; 11:660039. [PMID: 34249695 PMCID: PMC8261295 DOI: 10.3389/fonc.2021.660039] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/25/2021] [Indexed: 12/15/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is a rare and fatal disease of the pleural lining. Up to 80% of the MPM cases are linked to asbestos exposure. Even though its use has been banned in the industrialized countries, the cases continue to increase. MPM is a lethal cancer, with very little survival improvements in the last years, mirroring very limited therapeutic advances. Platinum-based chemotherapy in combination with pemetrexed and surgery are the standard of care, but prognosis is still unacceptably poor with median overall survival of approximately 12 months. The genomic landscape of MPM has been widely characterized showing a low mutational burden and the impairment of tumor suppressor genes. Among them, BAP1 and BLM are present as a germline inactivation in a small subset of patients and increases predisposition to tumorigenesis. Other studies have demonstrated a high frequency of mutations in DNA repair genes. Many therapy approaches targeting these alterations have emerged and are under evaluation in the clinic. High-throughput technologies have allowed the detection of more complex molecular events, like chromotripsis and revealed different transcriptional programs for each histological subtype. Transcriptional analysis has also paved the way to the study of tumor-infiltrating cells, thus shedding lights on the crosstalk between tumor cells and the microenvironment. The tumor microenvironment of MPM is indeed crucial for the pathogenesis and outcome of this disease; it is characterized by an inflammatory response to asbestos exposure, involving a variety of chemokines and suppressive immune cells such as M2-like macrophages and regulatory T cells. Another important feature of MPM is the dysregulation of microRNA expression, being frequently linked to cancer development and drug resistance. This review will give a detailed overview of all the above mentioned features of MPM in order to improve the understanding of this disease and the development of new therapeutic strategies.
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Affiliation(s)
- Stefanie Hiltbrunner
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
- Comprehensive Cancer Center Zurich, University of Zurich, Zurich, Switzerland
| | - Laura Mannarino
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milano, Italy
| | | | - Isabelle Opitz
- Department of Thoracic Surgery, University Hospital Zurich, Zurich, Switzerland
| | - Angelica Rigutto
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
- Comprehensive Cancer Center Zurich, University of Zurich, Zurich, Switzerland
| | - Alexander Laure
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
- Comprehensive Cancer Center Zurich, University of Zurich, Zurich, Switzerland
| | - Michela Lia
- Mesothelioma Unit, Azienda Ospedaliera SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Paolo Nozza
- Department of Pathology, Azienda Ospedaliera SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Antonio Maconi
- Infrastruttura Ricerca Formazione Innovazione (IRFI), Dipartimento Attività Integrate Ricerca e Innovazione (DAIRI), Azienda Ospedaliera SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Sergio Marchini
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milano, Italy
| | - Maurizio D’Incalci
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milano, Italy
| | - Alessandra Curioni-Fontecedro
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
- Comprehensive Cancer Center Zurich, University of Zurich, Zurich, Switzerland
| | - Federica Grosso
- Mesothelioma Unit, Azienda Ospedaliera SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
- Translational Medicine, Dipartimento Attività Integrate Ricerca e Innovazione (DAIRI), Azienda Ospedaliera SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
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Rapa I, Votta A, Giorcelli J, Izzo S, Rigutto A, Metovic J, Napoli F, Volante M. Proposal of a Panel of Genes Identified by miRNA Profiling as Candidate Prognostic Biomarkers in Lung Carcinoids. Neuroendocrinology 2021; 111:115-122. [PMID: 32040954 DOI: 10.1159/000506401] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 02/09/2020] [Indexed: 11/19/2022]
Abstract
AIM To validate the prognostic role of a panel of genes previously uncovered by our group to be specific targets of miRNAs differentially expressed in lung carcinoids with aggressive pathological features. METHODS Four genes, namely, cyclic AMP response element binding protein-1 (CREBP1), activin A receptor type 2B (ACVR2B), LIM homeobox 2 (LHX2), and Krüppel-like factor 12 (KLF12), were identified in a previous study by our group using in silico analysis to be regulated by 3 miRNAs (miR-409-3p, miR-409-5p, and miR-431-5p) that were shown to be downregulated in aggressive lung carcinoids. These genes were analyzed using real-time PCR in a cohort of 102 lung carcinoids. Fifty high-grade lung carcinomas served as control group. Their expression was correlated with the expression of miR-409-3p, miR-409-5p, and miR-431-5p and with clinical pathological parameters and disease-free survival. RESULTS The expression of all but CREBP1 gene was significantly different between lung carcinoids and high-grade neuroendocrine carcinomas. ACVR2B and LHX2 were significantly inversely correlated with miR-409-3p and miR-409-5p. High levels of ACVR2B and LHX2 were significantly associated with atypical histotype, high tumor grade, and higher proliferation Ki-67 index (all p < 0.05). Low levels of KLF12 were significantly associated with the presence of necrosis and positive nodal status (all p < 0.05). Finally, low KLF12 expression was associated with shorter disease-free survival in lung carcinoids as a whole and in atypical carcinoids, only (all p < 0.001). CONCLUSIONS ACVR2B, LHX2, and KFL12 are novel potential biomarkers associated with aggressive features in lung carcinoids.
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Affiliation(s)
- Ida Rapa
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Italy
| | - Arianna Votta
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Italy
| | - Jessica Giorcelli
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Italy
| | - Stefania Izzo
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Italy
| | - Angelica Rigutto
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Italy
| | - Jasna Metovic
- Department of Oncology, University of Turin, "Città della Salute e della Scienza" Hospital, Turin, Italy
| | - Francesca Napoli
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Italy
| | - Marco Volante
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Italy,
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Tabbò F, Guerrera F, Bironzo P, Gagliasso M, Cartia C, Rigutto A, Izzo S, Veneziano F, Arizio F, Ardissone F, Papotti M, Volante M, Novello S, Righi L. P2.09-18 Lymphocyte Infiltration Pattern and STING Expression Identify Different Prognostic Groups in Early Stage NSCLC. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.1667] [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: 11/24/2022]
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Tabbò F, Righi L, Rota G, Cappia S, Rigutto A, Izzo S, Novello S, Volante M. EP1.09-13 Clinic-Pathological and Molecular Features of PD-L1 Analyses in Advanced NSCLC: A Real Life Single Center Experience. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.2209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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