1
|
Bassani B, Simonetti G, Cancila V, Fiorino A, Ciciarello M, Piva A, Khorasani AM, Chiodoni C, Lecis D, Gulino A, Fonzi E, Botti L, Portararo P, Costanza M, Brambilla M, Colombo G, Schwaller J, Tzankov A, Ponzoni M, Ciceri F, Bolli N, Curti A, Tripodo C, Colombo MP, Sangaletti S. ZEB1 shapes AML immunological niches, suppressing CD8 T cell activity while fostering Th17 cell expansion. Cell Rep 2024; 43:113794. [PMID: 38363677 DOI: 10.1016/j.celrep.2024.113794] [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: 03/21/2023] [Revised: 11/07/2023] [Accepted: 01/30/2024] [Indexed: 02/18/2024] Open
Abstract
Acute myeloid leukemia (AML) progression is influenced by immune suppression induced by leukemia cells. ZEB1, a critical transcription factor in epithelial-to-mesenchymal transition, demonstrates immune regulatory functions in AML. Silencing ZEB1 in leukemic cells reduces engraftment and extramedullary disease in immune-competent mice, activating CD8 T lymphocytes and limiting Th17 cell expansion. ZEB1 in AML cells directly promotes Th17 cell development that, in turn, creates a self-sustaining loop and a pro-invasive phenotype, favoring transforming growth factor β (TGF-β), interleukin-23 (IL-23), and SOCS2 gene transcription. In bone marrow biopsies from AML patients, immunohistochemistry shows a direct correlation between ZEB1 and Th17. Also, the analysis of ZEB1 expression in larger datasets identifies two distinct AML groups, ZEB1high and ZEB1low, each with specific immunological and molecular traits. ZEB1high patients exhibit increased IL-17, SOCS2, and TGF-β pathways and a negative association with overall survival. This unveils ZEB1's dual role in AML, entwining pro-tumoral and immune regulatory capacities in AML blasts.
Collapse
Affiliation(s)
- Barbara Bassani
- Molecular Immunology Unit, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Giorgia Simonetti
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Valeria Cancila
- Tumor Immunology Unit, Department of Health Sciences, Human Pathology Section, School of Medicine, University of Palermo, 90133 Palermo, Italy
| | - Antonio Fiorino
- Predictive Medicine: Molecular Bases of Genetic Risk Unit, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Marilena Ciciarello
- CNR Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza," Unit of Bologna, Bologna, Italy; IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy; Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Annamaria Piva
- Molecular Immunology Unit, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Arman Mandegar Khorasani
- Molecular Immunology Unit, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Claudia Chiodoni
- Molecular Immunology Unit, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Daniele Lecis
- Molecular Immunology Unit, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | | | - Eugenio Fonzi
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori," Meldola, Forlì-Cesena, Italy
| | - Laura Botti
- Molecular Immunology Unit, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Paola Portararo
- Molecular Immunology Unit, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Massimo Costanza
- Neuro-Oncology Unit, Department of Clinical Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Marta Brambilla
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giorgia Colombo
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Juerg Schwaller
- University Children's Hospital Basel & Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Alexandar Tzankov
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Maurilio Ponzoni
- IRCCS Ospedale S. Raffaele, University Vita-Salute San Raffaele, Milan, Italy
| | - Fabio Ciceri
- IRCCS Ospedale S. Raffaele, University Vita-Salute San Raffaele, Milan, Italy
| | - Niccolò Bolli
- Hematology Division, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Antonio Curti
- Department of Experimental, Diagnostic and Specialty Medicine - DIMES, Institute of Hematology "Seràgnoli," Bologna, Italy
| | - Claudio Tripodo
- Tumor Immunology Unit, Department of Health Sciences, Human Pathology Section, School of Medicine, University of Palermo, 90133 Palermo, Italy; IFOM-ETS-The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Mario P Colombo
- Molecular Immunology Unit, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy.
| | - Sabina Sangaletti
- Molecular Immunology Unit, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy.
| |
Collapse
|
2
|
Ferrari A, Cangini D, Ghelli Luserna di Rorà A, Condorelli A, Pugliese M, Schininà G, Cosentino S, Fonzi E, Domizio C, Simonetti G, Leotta S, Milone G, Martinelli G. Venetoclax durable response in adult relapsed/refractory Philadelphia-negative acute lymphoblastic leukemia with JAK/STAT pathway alterations. Front Cell Dev Biol 2023; 11:1165308. [PMID: 37287455 PMCID: PMC10242111 DOI: 10.3389/fcell.2023.1165308] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/03/2023] [Indexed: 06/09/2023] Open
Abstract
High-risk relapsed/refractory adult Philadelphia-negative (Ph-) B-cell acute lymphoblastic leukemia (B-ALL) is a great challenge due to limited possibilities to achieve and maintain a complete response. This also applies to cases with extramedullary (EM) involvement that have poor outcomes and no accepted standard therapeutic approaches. The incidence of EM localization in relapsed/refractory B-ALL is poorly investigated: data on patients treated with blinatumomab reported a 40% rate. Some responses were reported in EM patients with relapsed/refractory B-ALL treated with inotuzumab ozogamicin or CAR-T. However, molecular mechanisms of response or refractoriness are usually investigated neither at the medullary nor at EM sites. In the complex scenario of pluri-relapsed/refractory B-ALL patients, new target therapies are needed. Our analysis started with the case of an adult pluri-relapsed Ph- B-ALL patient, poorly sensitive to inotuzumab ozogamicin, donor lymphocyte infusions, and blinatumomab in EM disease, who achieved a durable/complete response after treatment with the BCL2-inhibitor venetoclax. The molecular characterization of medullary and EM samples revealed a tyrosine kinase domain JAK1 mutation in the bone marrow and EM samples at relapse. By comparing the expression level of BCL2- and JAK/STAT pathway-related genes between the patient samples, 136 adult JAK1 wt B-ALL, and 15 healthy controls, we identified differentially expressed genes, including LIFR, MTOR, SOCS1/2, and BCL2/BCL2L1, that are variably modulated at diverse time points and might explain the prolonged response to venetoclax (particularly in the EM site, which was only partially affected by previous therapies). Our results suggest that the deep molecular characterization of both medullary and EM samples is fundamental to identifying effective and personalized targeted therapies.
Collapse
Affiliation(s)
- Anna Ferrari
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Delia Cangini
- Hematology Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Andrea Ghelli Luserna di Rorà
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
- Fondazione Pisana per Scienza ONLUS, Pisa, Italy
| | - Annalisa Condorelli
- Divisione di Ematologia con Trapianto Emopoietico—Azienda Ospedaliera Universitaria Policlinico “G. Rodolico- San Marco”, Catania, Italy
| | - Marta Pugliese
- Divisione di Ematologia con Trapianto Emopoietico—Azienda Ospedaliera Universitaria Policlinico “G. Rodolico- San Marco”, Catania, Italy
| | - Giovanni Schininà
- Divisione di Ematologia con Trapianto Emopoietico—Azienda Ospedaliera Universitaria Policlinico “G. Rodolico- San Marco”, Catania, Italy
| | | | - Eugenio Fonzi
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Chiara Domizio
- Department of Life Sciences and Biotechnology, Ferrara University, Ferrara, Italy
| | - Giorgia Simonetti
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Salvatore Leotta
- Divisione di Ematologia con Trapianto Emopoietico—Azienda Ospedaliera Universitaria Policlinico “G. Rodolico- San Marco”, Catania, Italy
| | - Giuseppe Milone
- Divisione di Ematologia con Trapianto Emopoietico—Azienda Ospedaliera Universitaria Policlinico “G. Rodolico- San Marco”, Catania, Italy
| | - Giovanni Martinelli
- Scientific Directorate, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| |
Collapse
|
3
|
Ferrari A, Fiocca R, Bonora E, Domizio C, Fonzi E, Angeli D, Domenico Raulli G, Mattioli S, Martinelli G, Molinari C. Detection of a Novel MSI2-C17orf64 Transcript in a Patient with Aggressive Adenocarcinoma of the Gastroesophageal Junction: A Case Report. Genes (Basel) 2023; 14:genes14040918. [PMID: 37107676 PMCID: PMC10137952 DOI: 10.3390/genes14040918] [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: 03/16/2023] [Revised: 04/06/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Adenocarcinoma of the esophagus (EAC) and gastroesophageal junction (GEJ-AC) is associated with poor prognosis, treatment resistance and limited systemic therapeutic options. To deeply understand the genomic landscape of this cancer type, and potentially identify a therapeutic target in a neoadjuvant chemotherapy non-responder 48-year-old man, we adopted a multi-omic approach. We simultaneously evaluated gene rearrangements, mutations, copy number status, microsatellite instability and tumor mutation burden. The patient displayed pathogenic mutations of the TP53 and ATM genes and variants of uncertain significance of three kinases genes (ERBB3, CSNK1A1 and RPS6KB2), along with FGFR2 and KRAS high copy number amplification. Interestingly, transcriptomic analysis revealed the Musashi-2 (MSI2)-C17orf64 fusion that has never been reported before. Rearrangements of the RNA-binding protein MSI2 with a number of partner genes have been described across solid and hematological tumors. MSI2 regulates several biological processes involved in cancer initiation, development and resistance to treatment, and deserves further investigation as a potential therapeutic target. In conclusion, our extensive genomic characterization of a gastroesophageal tumor refractory to all therapeutic approaches led to the discovery of the MSI2-C17orf64 fusion. The results underlie the importance of deep molecular analyses enabling the identification of novel patient-specific markers to be monitored during therapy or even targeted at disease evolution.
Collapse
Affiliation(s)
- Anna Ferrari
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, FC, Italy
| | - Roberto Fiocca
- Unit of Anatomic Pathology, Ospedale Policlinico San Martino IRCCS, 16125 Genova, Italy
- Department of Surgical and Diagnostic Sciences (DISC), University of Genova, 16125 Genova, Italy
| | - Elena Bonora
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum, University of Bologna, Via Massarenti 9, 40126 Bologna, Italy
| | - Chiara Domizio
- Department of Life Sciences and Biotechnology, Ferrara University, 44124 Ferrara, Italy
| | - Eugenio Fonzi
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, FC, Italy
| | - Davide Angeli
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, FC, Italy
| | | | - Sandro Mattioli
- GVM Care & Research Group, Division of Thoracic Surgery-Maria Cecilia Hospital, 48022 Cotignola, RA, Italy
- Alma Mater Studiorum-University of Bologna, 40126 Bologna, Italy
| | - Giovanni Martinelli
- Scientific Directorate, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, FC, Italy
| | - Chiara Molinari
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, FC, Italy
| |
Collapse
|
4
|
Vanni S, Fausti V, Fonzi E, Liverani C, Miserocchi G, Spadazzi C, Cocchi C, Calabrese C, Gurrieri L, Riva N, Recine F, Casadei R, Pieri F, Guerrieri AN, Serra M, Ibrahim T, Mercatali L, De Vita A. Unveiling the Genomic Basis of Chemosensitivity in Sarcomas of the Extremities: An Integrated Approach for an Unmet Clinical Need. Int J Mol Sci 2023; 24:ijms24086926. [PMID: 37108089 PMCID: PMC10138892 DOI: 10.3390/ijms24086926] [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: 02/28/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Myxofibrosarcoma (MFS) and undifferentiated pleomorphic sarcoma (UPS) can be considered as a spectrum of the same disease entity, representing one of the most common adult soft tissue sarcoma (STS) of the extremities. While MFS is rarely metastasizing, it shows an extremely high rate of multiple frequent local recurrences (50-60% of cases). On the other hand, UPS is an aggressive sarcoma prone to distant recurrence, which is correlated to a poor prognosis. Differential diagnosis is challenging due to their heterogeneous morphology, with UPS remaining a diagnosis of exclusion for sarcomas with unknown differentiation lineage. Moreover, both lesions suffer from the unavailability of diagnostic and prognostic biomarkers. In this context, a genomic approach combined with pharmacological profiling could allow the identification of new predictive biomarkers that may be exploited for differential diagnosis, prognosis and targeted therapy, with the aim to improve the management of STS patients. RNA-Seq analysis identified the up-regulation of MMP13 and WNT7B in UPS and the up-regulation of AKR1C2, AKR1C3, BMP7, and SGCG in MFS, which were confirmed by in silico analyses. Moreover, we identified the down-regulation of immunoglobulin genes in patient-derived primary cultures that responded to anthracycline treatment compared to non-responder cultures. Globally, the obtained data corroborated the clinical observation of UPS as an histotype refractory to chemotherapy and the key role of the immune system in determining chemosensitivity of these lesions. Moreover, our results confirmed the validity of genomic approaches for the identification of predictive biomarkers in poorly characterized neoplasms as well as the robustness of our patient-derived primary culture models in recapitulating the chemosensitivity features of STS. Taken as a whole, this body of evidence may pave the way toward an improvement of the prognosis of these rare diseases through a treatment modulation driven by a biomarker-based patient stratification.
Collapse
Affiliation(s)
- Silvia Vanni
- Preclinic and Osteoncology Unit, Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, Italy
| | - Valentina Fausti
- Clinical and Experimental Oncology, Immunotherapy, Rare Cancers and Biological Resource Center, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, Italy
| | - Eugenio Fonzi
- Biostatistics and Clinical Trials Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, Italy
| | - Chiara Liverani
- Preclinic and Osteoncology Unit, Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, Italy
| | - Giacomo Miserocchi
- Preclinic and Osteoncology Unit, Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, Italy
| | - Chiara Spadazzi
- Preclinic and Osteoncology Unit, Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, Italy
| | - Claudia Cocchi
- Preclinic and Osteoncology Unit, Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, Italy
| | - Chiara Calabrese
- Preclinic and Osteoncology Unit, Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, Italy
| | - Lorena Gurrieri
- Clinical and Experimental Oncology, Immunotherapy, Rare Cancers and Biological Resource Center, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, Italy
| | - Nada Riva
- Clinical and Experimental Oncology, Immunotherapy, Rare Cancers and Biological Resource Center, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, Italy
| | - Federica Recine
- Medical Oncology Unit, Azienda Ospedaliera "San Giovanni Addolorata", 00184 Roma, Italy
| | - Roberto Casadei
- General and Oncologic Surgery, "Morgagni-Pierantoni" Hospital, 47121 Forlì, Italy
| | - Federica Pieri
- Pathology Unit, "Morgagni-Pierantoni" Hospital, 47121 Forlì, Italy
| | - Ania Naila Guerrieri
- Osteoncologia, Sarcomi dell'osso e dei tessuti molli, e Terapie Innovative, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Massimo Serra
- Osteoncologia, Sarcomi dell'osso e dei tessuti molli, e Terapie Innovative, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Toni Ibrahim
- Osteoncologia, Sarcomi dell'osso e dei tessuti molli, e Terapie Innovative, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Laura Mercatali
- Preclinic and Osteoncology Unit, Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, Italy
| | - Alessandro De Vita
- Preclinic and Osteoncology Unit, Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, Italy
| |
Collapse
|
5
|
Ferrari A, Vitali S, Fonzi E, Di Rora AGL, Domizio C, Papayannidis C, Bochicchio MT, Marconi G, Dall'Olio D, Tebaldi M, Rondoni M, Giannini B, Giglio F, Pasciolla C, Fumagalli M, Galimberti S, Castellani G, Remondini D, Simonetti G, Martinelli G. Abstract 6163: Fusion landscape in acute leukemias: A submerged world of not routinely characterized transcripts. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-6163] [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: 04/07/2023]
Abstract
Abstract
Background: Fusions (Fs) are major molecular biological abnormalities in acute leukemias (ALs), and all well-known Fs in leukemias are founder variations are routinely used as molecular markers for the diagnosis, classification, risk stratification, and targeted therapy but there is a considerable part of ALs that are not screened for other known/unknown transcripts. For example in B-Other B Acute Lymphoblastic Leukemia (B-ALL) [Ph-/-/-; negative for t(9;22); t(1;19); t(4;11); 61% of adult B-ALL], many chimeric genes have been identified leading to a refined classification of B-ALL and to, in some cases, tailored therapies. At this point, a RNA-seq approach is needed but challenging for many aspects, among them a not standardized and very heterogeneous F data analysis.
Aims: We developed and validated our integrated pipeline in order to assess targetable biomarkers and to better classify patients (pts).
Methods: we performed 1385 gene RNAseq (Illumina) of 224 adult AL samples (112 Ph-/-/-, 41 Ph+, 6 t(1;19), 16 T-LBL/T-ALL and 49 AML). Starting from Ph-/-/-, we developed a combined 4 tool analysis that is further implemented with a filtering strategy with a specific ALs fusion literature filter (Patent PCTEP2021-065692 and 749 ALL Fs database copyright) (Fig.1A). We validate our strategy using: RT-PCR, FISH SNP Arrays; MLPA and total RNA-seq.
Results: From 3022 candidate Fs, we retained 160 of them (5.3%; excluding WHO canonical Fs) not otherwise detected, in 120 pts with a high Fs rate in T-LBL/T-ALL, Ph-/-/- and Ph+ (62.5%, 62.2% and 61% respectively) denoting that ALs are not deeply characterized (Fig 1B). The lower rate was found in AML (26.5%), but we were able to identify new ETV6 rearrangement (r) and a FISH cryptic F in a 46, XY pt (TBL1XR1-MECOM). We validated 98 Fs that have been already reported in the literature and 43 novel F transcripts. We obtained a validation rate of 81%. The majority of fused samples (65.2%) had only one detectable F while a smaller group was characterized by multiple Fs. Many of these Fs were previously described in B/T-ALL and AML (e.g. KMT2A-MLLT1, ABL1/2-RCSD1, IGH-MYC, NUP214-SET, ETV6-MECOM). In our bigger sub-cohort (Ph-/-/-), 44 Fs out of 109 (40.3%) were never been reported in Ph- ALL cases. In 15 Ph-like pts, we identified and validate 11 new transcripts. Ph-/-/- F detection help to sub-classify our fused pts in Ph-/-/- subgroups (ZNF384r-11.8%; Ph-like-19.1%; DUX4r- 4.4%; HLFr, MLLr and BCL2/MYC in 2.9%; MEF2Dr-1.5%).
Conclusions: we identified pivotal transcripts in all ALs and an unexpected high rate of secondary Fs in adult ALs subgroups (52.4%) that are not characterized with conventional diagnostic methods. The use of an NGS approach and a powerful pipeline permit us to detect Fs useful for a better classification, prognostic identification (e.g. TBL1XR1-MECOM) and in some cases to find targetable Fs (e.g. ABL1-2/RCSD1, NUMA1-CSF1R, ZMYM2-FLT3). Supported by: L3P2505.
Citation Format: Anna Ferrari, Silvia Vitali, Eugenio Fonzi, Andrea Ghelli Luserna Di Rora, Chiara Domizio, Cristina Papayannidis, Maria Teresa Bochicchio, Giovanni Marconi, Daniele Dall'Olio, Michela Tebaldi, Michela Rondoni, Barbara Giannini, Fabio Giglio, Crescenza Pasciolla, Monica Fumagalli, Sara Galimberti, Gastone Castellani, Daniel Remondini, Giorgia Simonetti, Giovanni Martinelli. Fusion landscape in acute leukemias: A submerged world of not routinely characterized transcripts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6163.
Collapse
Affiliation(s)
- Anna Ferrari
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) - IRCCS, Meldola, Italy
| | - Silvia Vitali
- 2Dipartimento di Fisica e Astronomia, INFN, Università di Bologna, Bologna, Italy
| | - Eugenio Fonzi
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) - IRCCS, Meldola, Italy
| | | | - Chiara Domizio
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) - IRCCS, Meldola, Italy
| | - Cristina Papayannidis
- 3IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli” Bologna, Bologna, Italy
| | - Maria Teresa Bochicchio
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) - IRCCS, Meldola, Italy
| | - Giovanni Marconi
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) - IRCCS, Meldola, Italy
| | - Daniele Dall'Olio
- 2Dipartimento di Fisica e Astronomia, INFN, Università di Bologna, Bologna, Italy
| | - Michela Tebaldi
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) - IRCCS, Meldola, Italy
| | - Michela Rondoni
- 4Hematology Unit & Romagna Transplant Network, Ravenna Hospital, Ravenna, Italy
| | - Barbara Giannini
- 5Laboratorio Unico- AUSL della Romagna Pievesestina di Cesena (FC), Cesena, Italy
| | - Fabio Giglio
- 6Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Crescenza Pasciolla
- 7Hematology and Bone Marrow Transplantation Unit, Istituto Oncologico IRCCS “Giovanni Paolo II”, Bari, Italy
| | | | | | - Gastone Castellani
- 2Dipartimento di Fisica e Astronomia, INFN, Università di Bologna, Bologna, Italy
| | - Daniel Remondini
- 2Dipartimento di Fisica e Astronomia, INFN, Università di Bologna, Bologna, Italy
| | - Giorgia Simonetti
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) - IRCCS, Meldola, Italy
| | - Giovanni Martinelli
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) - IRCCS, Meldola, Italy
| |
Collapse
|
6
|
Ghetti M, Padella A, Fonzi E, Ledda L, Lusernadi Rorà AG, Paganelli M, Tolomeo D, Storlazzi CT, Martinelli G, Simonetti G. Abstract 1555: circPVT1 and linear PVT1 isoforms regulate cell growth, metabolic and DNA damage response related gene signatures in acute myeloid leukemia. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1555] [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
Non-coding (nc)RNAs, including circular (circ)RNAs, contribute to tumor development and progression. Several ncRNAs were shown to affect the onset, prognosis, and treatment of acute myeloid leukemia (AML) in the past years. The human Plasmacytoma Variant Translocation 1 (PVT1) gene maps on the long arm of chromosome 8 (8q24), in the same genomic region hosting MYC and encoding for 83 linear (PVT1, lncipedia.org) and 26 high-confidence circular isoforms (circPVT1, www.circbase.org). The most common isoform of circPVT1 is a product of back-splicing of 410 nt and contains the whole exon 2 of PVT1 in a closed loop-like structure (hsa_circ_0001821). The study aims to investigate the role of PVT1 isoforms and circPVT1 in AML. Firstly, we focused on the various PVT1 isoforms and their differential expression in leukemia. Fourteen out of the 83 linear isoforms are expressed in the hematopoietic tissues (lymph node and white blood cells, www.noncode.org), and 6 of them were detectable in AML cell lines, including the t(8;21) KASUMI-1 and the NPM1-mutated OCI-AML3 models, together with circPVT1. We designed two antisense-oligonucleotides (ASOs), mapping on common exonic region and targeting the linear isoforms expressed in OCI-AML3 and KASUMI-1 cells, and one ASO spanning the junction region of circPVT1. ASOs-mediated knockdown (KD) showed a relevant decrease of PVT1 signals, especially by ASO combination, and circPVT1 level using the specific ASO in both cell lines, under normoxia and hypoxia (1% O2). The downregulation led to a significant decrease in cell growth, but, interestingly, only circPVT1-KD induced apoptosis under both conditions in OCI-AML3. To further investigate the biological consequences of circPVT1-KD, we performed RNAseq assays. Data analysis was performed by pseudo alignment of paired-end reads to the human transcriptome, then counted with the Kallisto tool. Differential expression analysis of single isoforms was performed with the Sleuth tool on normalized transcript per million. We identified a core of 644 and 838 commonly regulated genes by circPVT1 in both cell lines under normoxia and hypoxia, respectively. Pathway analysis (performed by EnrichR) revealed that these genes are involved not only in the RNA regulatory pathways, as expected according to circRNA functions, but also in metabolic (e.g., KDM3A, GPI, NFKBA, RBM3, XBP1) and DNA damage response (e.g., PIDD1, MUC1, BCLAF1, BABAM2) pathways, opening a new scenario for synthetic lethality approaches. In conclusion, our findings show that silencing of circPVT1 or the predominantly expressed PVT1 isoforms dampens leukemia cell growth, indicating a role in AML pathogenesis, and suggest that targeting them may have therapeutic potentials in AML.
Citation Format: Martina Ghetti, Antonella Padella, Eugenio Fonzi, Lorenzo Ledda, Andrea Ghelli Lusernadi Rorà, Matteo Paganelli, Doron Tolomeo, Clelia Tiziana Storlazzi, Giovanni Martinelli, Giorgia Simonetti. circPVT1 and linear PVT1 isoforms regulate cell growth, metabolic and DNA damage response related gene signatures in acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1555.
Collapse
Affiliation(s)
- Martina Ghetti
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori "Dino Amadori", Meldola, Italy
| | - Antonella Padella
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori "Dino Amadori", Meldola, Italy
| | - Eugenio Fonzi
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori "Dino Amadori", Meldola, Italy
| | - Lorenzo Ledda
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori "Dino Amadori", Meldola, Italy
| | | | - Matteo Paganelli
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori "Dino Amadori", Meldola, Italy
| | | | | | - Giovanni Martinelli
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori "Dino Amadori", Meldola, Italy
| | - Giorgia Simonetti
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori "Dino Amadori", Meldola, Italy
| |
Collapse
|
7
|
Ulivi P, Urbini M, Petracci E, Canale M, Dubini A, Bartolini D, Calistri D, Cravero P, Fonzi E, Martinelli G, Priano I, Andrikou K, Bronte G, Crinò L, Delmonte A. Wide Next-Generation Sequencing Characterization of Young Adults Non-Small-Cell Lung Cancer Patients. Cancers (Basel) 2022; 14:cancers14102352. [PMID: 35625958 PMCID: PMC9139648 DOI: 10.3390/cancers14102352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 12/01/2022] Open
Abstract
Molecular characterization of advanced non-small-cell lung cancer (NSCLC) is mandatory before any treatment decision making. Next-generation sequencing (NGS) approaches represent the best strategy in this context. The turnaround time for NGS methodologies and the related costs are becoming more and more adaptable for their use in clinical practice. In our study, we analyzed a case series of young (under 65 years old) NSCLC patients with a wide NGS gene panel assay. The most frequent altered genes were TP53 (64.55%), followed by KRAS (44.1%), STK11 (26.9%), CDKN2A (21.5%), CDKN2B (14.0%), EGFR (16.1%), and RB1 (10.8%). Tumor mutational burden (TMB) was also evaluated. Considering the cut-off of 10 mut/Mb, 62 (68.9%) patients showed a TMB < 10 mut/Mb, whereas 28 (31.1%) showed a TMB ≥ 10 mut/Mb. STK11 and KRAS mutations were significantly associated with a higher TMB (p = 0.019 and p = 0.004, respectively). Conversely, EGFR and EML4-ALK alterations were more frequently found in tumors with low TMB (p = 0.019 and p < 0.001, respectively). We compared results obtained from this approach with those obtained from a single or few genes approach, observing perfect concordance of the results.
Collapse
Affiliation(s)
- Paola Ulivi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (P.U.); (M.U.); (D.C.)
| | - Milena Urbini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (P.U.); (M.U.); (D.C.)
| | - Elisabetta Petracci
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.P.); (E.F.)
| | - Matteo Canale
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (P.U.); (M.U.); (D.C.)
- Correspondence: ; Tel.: +39-0543-739232; Fax: +39-0543-739221
| | | | | | - Daniele Calistri
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (P.U.); (M.U.); (D.C.)
| | - Paola Cravero
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (P.C.); (G.M.); (I.P.); (K.A.); (G.B.); (L.C.); (A.D.)
| | - Eugenio Fonzi
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.P.); (E.F.)
| | - Giovanni Martinelli
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (P.C.); (G.M.); (I.P.); (K.A.); (G.B.); (L.C.); (A.D.)
| | - Ilaria Priano
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (P.C.); (G.M.); (I.P.); (K.A.); (G.B.); (L.C.); (A.D.)
| | - Kalliopi Andrikou
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (P.C.); (G.M.); (I.P.); (K.A.); (G.B.); (L.C.); (A.D.)
| | - Giuseppe Bronte
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (P.C.); (G.M.); (I.P.); (K.A.); (G.B.); (L.C.); (A.D.)
| | - Lucio Crinò
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (P.C.); (G.M.); (I.P.); (K.A.); (G.B.); (L.C.); (A.D.)
| | - Angelo Delmonte
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (P.C.); (G.M.); (I.P.); (K.A.); (G.B.); (L.C.); (A.D.)
| |
Collapse
|
8
|
Simonetti G, Mengucci C, Padella A, Fonzi E, Picone G, Delpino C, Nanni J, De Tommaso R, Franchini E, Papayannidis C, Marconi G, Pazzaglia M, Perricone M, Scarpi E, Fontana MC, Bruno S, Tebaldi M, Ferrari A, Bochicchio MT, Ghelli Luserna Di Rorà A, Ghetti M, Napolitano R, Astolfi A, Baldazzi C, Guadagnuolo V, Ottaviani E, Iacobucci I, Cavo M, Castellani G, Haferlach T, Remondini D, Capozzi F, Martinelli G. Integrated genomic-metabolic classification of acute myeloid leukemia defines a subgroup with NPM1 and cohesin/DNA damage mutations. Leukemia 2021; 35:2813-2826. [PMID: 34193978 PMCID: PMC8478658 DOI: 10.1038/s41375-021-01318-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 03/11/2021] [Revised: 05/21/2021] [Accepted: 06/02/2021] [Indexed: 02/06/2023]
Abstract
Although targeting of cell metabolism is a promising therapeutic strategy in acute myeloid leukemia (AML), metabolic dependencies are largely unexplored. We aimed to classify AML patients based on their metabolic landscape and map connections between metabolic and genomic profiles. Combined serum and urine metabolomics improved AML characterization compared with individual biofluid analysis. At intracellular level, AML displayed dysregulated amino acid, nucleotide, lipid, and bioenergetic metabolism. The integration of intracellular and biofluid metabolomics provided a map of alterations in the metabolism of polyamine, purine, keton bodies and polyunsaturated fatty acids and tricarboxylic acid cycle. The intracellular metabolome distinguished three AML clusters, correlating with distinct genomic profiles: NPM1-mutated(mut), chromatin/spliceosome-mut and TP53-mut/aneuploid AML that were confirmed by biofluid analysis. Interestingly, integrated genomic-metabolic profiles defined two subgroups of NPM1-mut AML. One was enriched for mutations in cohesin/DNA damage-related genes (NPM1/cohesin-mut AML) and showed increased serum choline + trimethylamine-N-oxide and leucine, higher mutation load, transcriptomic signatures of reduced inflammatory status and better ex-vivo response to EGFR and MET inhibition. The transcriptional differences of enzyme-encoding genes between NPM1/cohesin-mut and NPM1-mut allowed in silico modeling of intracellular metabolic perturbations. This approach predicted alterations in NAD and purine metabolism in NPM1/cohesin-mut AML that suggest potential vulnerabilities, worthy of being therapeutically explored.
Collapse
Affiliation(s)
- Giorgia Simonetti
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy.
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.
| | - Carlo Mengucci
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, FC, Italy
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Antonella Padella
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy.
| | - Eugenio Fonzi
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Gianfranco Picone
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, FC, Italy
| | - Claudio Delpino
- Departamento de Ingeniería Química, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Jacopo Nanni
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Rossella De Tommaso
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Eugenia Franchini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Cristina Papayannidis
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Giovanni Marconi
- Hematology Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Martina Pazzaglia
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Margherita Perricone
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Emanuela Scarpi
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Maria Chiara Fontana
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Samantha Bruno
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Michela Tebaldi
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Anna Ferrari
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Maria Teresa Bochicchio
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | | | - Martina Ghetti
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Roberta Napolitano
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Annalisa Astolfi
- Giorgio Prodi" Cancer Research Center, University of Bologna, Bologna and Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, Ferrara, Italy
| | - Carmen Baldazzi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Viviana Guadagnuolo
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Emanuela Ottaviani
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michele Cavo
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Gastone Castellani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | | | - Daniel Remondini
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Francesco Capozzi
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, FC, Italy
| | - Giovanni Martinelli
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| |
Collapse
|
9
|
De Vita A, Ferrari A, Miserocchi G, Vanni S, Domizio C, Fonzi E, Fausti V, Recine F, Bassi M, Campobassi A, Liverani C, Spadazzi C, Cocchi C, De Luca G, Pieri F, Gurrieri L, Di Menna G, Calpona S, Bongiovanni A, Martinelli G, Ibrahim T, Mercatali L. Identification of a novel RAB3IP-HMGA2 fusion transcript in an adult head and neck rhabdomyosarcoma. Oral Dis 2021; 28:2052-2054. [PMID: 34592033 DOI: 10.1111/odi.14036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 09/02/2021] [Accepted: 09/13/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Alessandro De Vita
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Anna Ferrari
- Biosciences Laboratory, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Giacomo Miserocchi
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Silvia Vanni
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Chiara Domizio
- Biosciences Laboratory, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Eugenio Fonzi
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Valentina Fausti
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Federica Recine
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy.,Medical Oncology Unit, Azienda Ospedaliera San Giovanni Addolorata, Roma, Italy
| | - Massimo Bassi
- Maxillofacial Surgery Unit, Bufalini Hospital, Cesena, Italy
| | | | - Chiara Liverani
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Chiara Spadazzi
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Claudia Cocchi
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | | | - Federica Pieri
- Pathology Unit, Morgagni-Pierantoni Hospital, Forlì, Italy
| | - Lorena Gurrieri
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Giandomenico Di Menna
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Sebastiano Calpona
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Alberto Bongiovanni
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Giovanni Martinelli
- Scientific Directorate, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Toni Ibrahim
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Laura Mercatali
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| |
Collapse
|
10
|
Bravaccini S, Fonzi E, Tebaldi M, Angeli D, Martinelli G, Nicolini F, Parrella P, Mazza M. Abstract 709: Estrogen and androgen receptor inhibitors: Unexpected allies in the fight against COVID-19. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-709] [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
IntroductionGiven the COVID-19 coronavirus emergency, a special focus is needed on the impact of this rapidly spreading viral infection on cancer patients. No prophylactic treatments for COVID-19 have been clearly proven and found. In this pandemic context, cancer patients constitute a particularly fragile population that would benefit the best from such treatments, a present unmet need. TMPRSS2 is essential for COVID-19 replication cycle and it is under androgen control. Estrogen and androgen receptor dependent cues converge on TMPRSS2 regulation through different mechanisms of action that can be blocked by the use of hormonal therapies. Androgen receptor (AR) signaling in the TMPRSS2 regulation is emerging as an important determinant of SARS-CoV-2 susceptibility.
Materials and MethodsIn our study, we analyzed AR and TMPRSS2 expression in 17352 normal and 9556 cancer tissues from public repositories and stratified data according to sex and age. Gene expression data were retrieved from TCGA and Genotype-Tissue Expression (GTEx) portal. Differences in gene expression were tested with Mann-Whitney U-test.
ResultsThe emerging picture is that some patient groups may be particularly susceptible to SARS-CoV-2 infection and may benefit from anti-androgen or anti-estrogen based therapies. Indeed, while young individuals showed a coherent reduction of AR expression in tumors as compared to healthy tissues regardless of gender, elderly females showed increased AR levels in tumors compared to normal tissues. Coherently with AR overexpression, we also observed a significant increase in TMPRSS2 gene expression in tumors from elderly females with respect to age-matched normal tissues. These results highlight that cancers of elderly females have typically higher expression of AR and of TMPRSS2 identifying a population of cancer patients that may be particularly susceptible to COVID-19 infection.
These findings are relevant to choose proper treatments in order to protect cancer patients from concomitant SARS-CoV-2 contagion and related symptoms and put forward the idea that hormonal therapies could be used as prophylactic agents against COVID-19.
ConclusionsWe believe that there is enough body of evidence to foresee a prophylactic use of hormonal therapies against COVID-19 and this hypothesis can be easily tested on cohorts of breast and prostate cancer patients who follow those regimens. In case of pandemic, if the protective effect of hormonal therapies will be proven on cancer patients, the use of specific hormonal therapies could be extended to other oncological groups and to healthy individuals to decrease the overall risk of infection by SARS-CoV-2.
Citation Format: Sara Bravaccini, Eugenio Fonzi, Michela Tebaldi, Davide Angeli, Giovanni Martinelli, Fabio Nicolini, Paola Parrella, Massimiliano Mazza. Estrogen and androgen receptor inhibitors: Unexpected allies in the fight against COVID-19 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 709.
Collapse
Affiliation(s)
- Sara Bravaccini
- 1IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Eugenio Fonzi
- 1IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Michela Tebaldi
- 1IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Davide Angeli
- 1IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Giovanni Martinelli
- 1IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Fabio Nicolini
- 1IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Paola Parrella
- 2Fondazione IRCCS Casa Sollievo della Sofferenza Laboratorio di Oncologia, San Giovanni Rotondo, FG, Italy
| | - Massimiliano Mazza
- 1IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| |
Collapse
|
11
|
Simonetti G, Angeli D, Petracci E, Fonzi E, Vedovato S, Sperotto A, Padella A, Ghetti M, Ferrari A, Robustelli V, Di Liddo R, Conconi MT, Papayannidis C, Cerchione C, Rondoni M, Astolfi A, Ottaviani E, Martinelli G, Gottardi M. Adrenomedullin Expression Characterizes Leukemia Stem Cells and Associates With an Inflammatory Signature in Acute Myeloid Leukemia. Front Oncol 2021; 11:684396. [PMID: 34150648 PMCID: PMC8208888 DOI: 10.3389/fonc.2021.684396] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022] Open
Abstract
Adrenomedullin (ADM) is a hypotensive and vasodilator peptide belonging to the calcitonin gene-related peptide family. It is secreted in vitro by endothelial cells and vascular smooth muscle cells, and is significantly upregulated by a number of stimuli. Moreover, ADM participates in the regulation of hematopoietic compartment, solid tumors and leukemias, such as acute myeloid leukemia (AML). To better characterize ADM involvement in AML pathogenesis, we investigated its expression during human hematopoiesis and in leukemic subsets, based on a morphological, cytogenetic and molecular characterization and in T cells from AML patients. In hematopoietic stem/progenitor cells and T lymphocytes from healthy subjects, ADM transcript was barely detectable. It was expressed at low levels by megakaryocytes and erythroblasts, while higher levels were measured in neutrophils, monocytes and plasma cells. Moreover, cells populating the hematopoietic niche, including mesenchymal stem cells, showed to express ADM. ADM was overexpressed in AML cells versus normal CD34+ cells and in the subset of leukemia compared with hematopoietic stem cells. In parallel, we detected a significant variation of ADM expression among cytogenetic subgroups, measuring the highest levels in inv(16)/t(16;16) or complex karyotype AML. According to the mutational status of AML-related genes, the analysis showed a lower expression of ADM in FLT3-ITD, NPM1-mutated AML and FLT3-ITD/NPM1-mutated cases compared with wild-type ones. Moreover, ADM expression had a negative impact on overall survival within the favorable risk class, while showing a potential positive impact within the subgroup receiving a not-intensive treatment. The expression of 135 genes involved in leukemogenesis, regulation of cell proliferation, ferroptosis, protection from apoptosis, HIF-1α signaling, JAK-STAT pathway, immune and inflammatory responses was correlated with ADM levels in the bone marrow cells of at least two AML cohorts. Moreover, ADM was upregulated in CD4+ T and CD8+ T cells from AML patients compared with healthy controls and some ADM co-expressed genes participate in a signature of immune tolerance that characterizes CD4+ T cells from leukemic patients. Overall, our study shows that ADM expression in AML associates with a stem cell phenotype, inflammatory signatures and genes related to immunosuppression, all factors that contribute to therapy resistance and disease relapse.
Collapse
Affiliation(s)
- Giorgia Simonetti
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Davide Angeli
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Elisabetta Petracci
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Eugenio Fonzi
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Susanna Vedovato
- Department of Clinical and Experimental Medicine, University of Padova, Padua, Italy
| | - Alessandra Sperotto
- Hematology and Transplant Center Unit, Dipartimento di Area Medica (DAME), Udine University Hospital, Udine, Italy
| | - Antonella Padella
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Martina Ghetti
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Anna Ferrari
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Valentina Robustelli
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, Bologna, Italy
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Università di Bologna, Bologna, Italy
| | - Rosa Di Liddo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padua, Italy
| | - Maria Teresa Conconi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padua, Italy
| | - Cristina Papayannidis
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, Bologna, Italy
| | - Claudio Cerchione
- Hematology Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Michela Rondoni
- Hematology Unit & Romagna Transplant Network, Ravenna Hospital, Ravenna, Italy
| | - Annalisa Astolfi
- “Giorgio Prodi” Cancer Research Center, University of Bologna, Bologna, Italy
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Emanuela Ottaviani
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, Bologna, Italy
| | - Giovanni Martinelli
- Scientific Directorate, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Michele Gottardi
- Onco Hematology, Department of Oncology, Veneto Institute of Oncology IOV, IRCCS, Padua, Italy
| |
Collapse
|
12
|
Dall'Olio D, Curti N, Fonzi E, Sala C, Remondini D, Castellani G, Giampieri E. Correction to: Impact of concurrency on the performance of a whole exome sequencing pipeline. BMC Bioinformatics 2021; 22:292. [PMID: 34074241 PMCID: PMC8170930 DOI: 10.1186/s12859-021-04205-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Daniele Dall'Olio
- Department of Physics and Astronomy, University of Bologna, 40127, Bologna, BO, Italy
| | - Nico Curti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, BO, Italy
| | - Eugenio Fonzi
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014, Meldola, Italy
| | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, 40127, Bologna, BO, Italy.
| | - Daniel Remondini
- Department of Physics and Astronomy, University of Bologna, 40127, Bologna, BO, Italy
| | - Gastone Castellani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, BO, Italy
| | - Enrico Giampieri
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, BO, Italy
| |
Collapse
|
13
|
Bravaccini S, Fonzi E, Tebaldi M, Angeli D, Martinelli G, Nicolini F, Parrella P, Mazza M. Estrogen and Androgen Receptor Inhibitors: Unexpected Allies in the Fight Against COVID-19. Cell Transplant 2021; 30:963689721991477. [PMID: 33522308 PMCID: PMC7863556 DOI: 10.1177/0963689721991477] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Translational Relevance No prophylactic treatments for COVID-19 have been clearly proven and found. In this pandemic context, cancer patients constitute a particularly fragile population that would benefit the best from such treatments, a present unmet need. TMPRSS2 is essential for COVID-19 replication cycle and it is under androgen control. Estrogen and androgen receptor dependent cues converge on TMPRSS2 regulation through different mechanisms of action that can be blocked by the use of hormonal therapies. We believe that there is enough body of evidence to foresee a prophylactic use of hormonal therapies against COVID-19 and this hypothesis can be easily tested on cohorts of breast and prostate cancer patients who follow those regimens. In case of pandemic, if the protective effect of hormonal therapies will be proven on cancer patients, the use of specific hormonal therapies could be extended to other oncological groups and to healthy individuals to decrease the overall risk of infection by SARS-CoV-2. Given the COVID-19 coronavirus emergency, a special focus is needed on the impact of this rapidly spreading viral infection on cancer patients. Androgen receptor (AR) signaling in the transmembrane protease serine 2 (TMPRSS2) regulation is emerging as an important determinant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) susceptibility. In our study, we analyzed AR and TMPRSS2 expression in 17,352 normal and 9,556 cancer tissues from public repositories and stratified data according to sex and age. The emerging picture is that some patient groups may be particularly susceptible to SARS-CoV-2 infection and may benefit from antiandrogen- or tamoxifen-based therapies. These findings are relevant to choose proper treatments in order to protect cancer patients from concomitant SARS-CoV-2 contagion and related symptoms and put forward the idea that hormonal therapies could be used as prophylactic agents against COVID-19.
Collapse
Affiliation(s)
- Sara Bravaccini
- Bioscience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Eugenio Fonzi
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Michela Tebaldi
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Davide Angeli
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Giovanni Martinelli
- Bioscience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Fabio Nicolini
- Immunotherapy, Cell Therapy and Biobank (ITCB), IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Paola Parrella
- Fondazione IRCCS Casa Sollievo della Sofferenza Laboratorio di Oncologia, San Giovanni Rotondo, FG, Italy
| | - Massimiliano Mazza
- Immunotherapy, Cell Therapy and Biobank (ITCB), IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| |
Collapse
|
14
|
Dall'Olio D, Curti N, Fonzi E, Sala C, Remondini D, Castellani G, Giampieri E. Impact of concurrency on the performance of a whole exome sequencing pipeline. BMC Bioinformatics 2021; 22:60. [PMID: 33563206 PMCID: PMC7874478 DOI: 10.1186/s12859-020-03780-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 09/24/2020] [Indexed: 11/12/2022] Open
Abstract
Background Current high-throughput technologies—i.e. whole genome sequencing, RNA-Seq, ChIP-Seq, etc.—generate huge amounts of data and their usage gets more widespread with each passing year. Complex analysis pipelines involving several computationally-intensive steps have to be applied on an increasing number of samples. Workflow management systems allow parallelization and a more efficient usage of computational power. Nevertheless, this mostly happens by assigning the available cores to a single or few samples’ pipeline at a time. We refer to this approach as naive parallel strategy (NPS). Here, we discuss an alternative approach, which we refer to as concurrent execution strategy (CES), which equally distributes the available processors across every sample’s pipeline. Results Theoretically, we show that the CES results, under loose conditions, in a substantial speedup, with an ideal gain range spanning from 1 to the number of samples. Also, we observe that the CES yields even faster executions since parallelly computable tasks scale sub-linearly. Practically, we tested both strategies on a whole exome sequencing pipeline applied to three publicly available matched tumour-normal sample pairs of gastrointestinal stromal tumour. The CES achieved speedups in latency up to 2–2.4 compared to the NPS. Conclusions Our results hint that if resources distribution is further tailored to fit specific situations, an even greater gain in performance of multiple samples pipelines execution could be achieved. For this to be feasible, a benchmarking of the tools included in the pipeline would be necessary. It is our opinion these benchmarks should be consistently performed by the tools’ developers. Finally, these results suggest that concurrent strategies might also lead to energy and cost savings by making feasible the usage of low power machine clusters.
Collapse
Affiliation(s)
- Daniele Dall'Olio
- Department of Physics and Astronomy, University of Bologna, 40127, Bologna, BO, Italy
| | - Nico Curti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, BO, Italy
| | - Eugenio Fonzi
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014, Meldola, Italy
| | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, 40127, Bologna, BO, Italy.
| | - Daniel Remondini
- Department of Physics and Astronomy, University of Bologna, 40127, Bologna, BO, Italy
| | - Gastone Castellani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, BO, Italy
| | - Enrico Giampieri
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, BO, Italy
| |
Collapse
|
15
|
Padella A, Fontana MC, Marconi G, Fonzi E, Petracci E, Ferrari A, Baldazzi C, Papayannidis C, Ghelli Luserna Di Rorá A, Testoni N, Castellani G, Haferlach T, Martinelli G, Simonetti G. Loss of PALB2 predicts poor prognosis in acute myeloid leukemia and suggests novel therapeutic strategies targeting the DNA repair pathway. Blood Cancer J 2021; 11:7. [PMID: 33414401 PMCID: PMC7791026 DOI: 10.1038/s41408-020-00396-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/16/2020] [Accepted: 11/27/2020] [Indexed: 12/21/2022] Open
Affiliation(s)
- Antonella Padella
- Istituto Scientifico Romagnolo per lo Studio e Cura dei Tumori (IRST) IRCCS, Meldola, Italy.
| | - Maria Chiara Fontana
- Istituto Scientifico Romagnolo per lo Studio e Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Giovanni Marconi
- Azienda Ospedaliero-Universitaria di Bologna, via Albertoni 15, Bologna, Italia, Istituto di Ematologia "Seràgnoli", Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Università degli Studi, Bologna, Italia
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Istituto di Ematologia "Seràgnoli", Università degli Studi, Bologna, Italy
| | - Eugenio Fonzi
- Istituto Scientifico Romagnolo per lo Studio e Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Elisabetta Petracci
- Istituto Scientifico Romagnolo per lo Studio e Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Anna Ferrari
- Istituto Scientifico Romagnolo per lo Studio e Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Carmen Baldazzi
- Azienda Ospedaliero-Universitaria di Bologna, via Albertoni 15, Bologna, Italia, Istituto di Ematologia "Seràgnoli", Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Università degli Studi, Bologna, Italia
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Istituto di Ematologia "Seràgnoli", Università degli Studi, Bologna, Italy
| | - Cristina Papayannidis
- Azienda Ospedaliero-Universitaria di Bologna, via Albertoni 15, Bologna, Italia, Istituto di Ematologia "Seràgnoli", Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Università degli Studi, Bologna, Italia
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Istituto di Ematologia "Seràgnoli", Università degli Studi, Bologna, Italy
| | | | - Nicoletta Testoni
- Azienda Ospedaliero-Universitaria di Bologna, via Albertoni 15, Bologna, Italia, Istituto di Ematologia "Seràgnoli", Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Università degli Studi, Bologna, Italia
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Istituto di Ematologia "Seràgnoli", Università degli Studi, Bologna, Italy
| | - Gastone Castellani
- Azienda Ospedaliero-Universitaria di Bologna, via Albertoni 15, Bologna, Italia, Istituto di Ematologia "Seràgnoli", Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Università degli Studi, Bologna, Italia
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Istituto di Ematologia "Seràgnoli", Università degli Studi, Bologna, Italy
| | | | - Giovanni Martinelli
- Istituto Scientifico Romagnolo per lo Studio e Cura dei Tumori (IRST) IRCCS, Meldola, Italy.
| | - Giorgia Simonetti
- Istituto Scientifico Romagnolo per lo Studio e Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| |
Collapse
|
16
|
Rocca A, Ravaioli S, Fonzi E, Barozzi I, Perone Y, Magnani L, Pirini F, Martinelli G, Bravaccini S. Abstract P4-07-06: Breast cancer subtype classification using NanoString and RNAseq technologies. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p4-07-06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Immunohistochemistry (IHC) is conventionally used in clinical practice to define Breast Cancer (BC) subtypes, while PAM50 is useful in specific cases. The former is partly subjective and semi-quantitative, the latter is based on gene expression profile. We compared gene expression data obtained by NanoString BC 360™ panel with those obtained by RNAseq on 12 Formalin-Fixed Paraffin-Embedded (FFPE) BC samples.
Methods: RNA was isolated from FFPE tumors and the quality was checked before performing NanoString BC 360™ assay and preparing RNAseq library (NEBNext Ultra II RNA Library Prep Kit, Illumina) following the manufacturers’ instructions. Libraries were sequenced on NextSeq500 (Illumina). Reads were aligned using Kallisto and raw read counts were normalized as Transcripts Per Million (TPM). PAM50 and Tumor Inflammation Signature (TIS) were determined on NanoString data. Two-sided t-test on TPM and on normalized NanoString counts was used to compare luminal and Triple Negative (TN) BCs (p <0.05 statistically significant), considering the 734 genes shared by the 2 assays. Deseq2 (1.22.1) was used to perform a differential gene expression analysis on raw RNAseq counts. Enrichment tests were performed on KEGG pathways (FDR < 0.05). Python and R softwares were used for statistical analyses.
Results: Of the 12 BC samples, 3 were luminal A-like, 3 luminal B (HER2+)-like and 6 TN by IHC (Table 1). Pearson’s correlation coefficient between NanoString counts and RNAseq TPM was 0.72.
Out of the 734 genes shared by both methods, those differentially expressed between luminal and TN BCs, defined based on IHC, were 135 according to RNAseq TPM, 155 according to NanoString counts and 88 according to both methods. These 88 genes belonged to “cell cycle”, “pathways in cancer”, “HIF-1 signaling”, “progesterone-mediated oocyte maturation”, “prostate cancer” and “basal cell carcinoma” KEGG pathways.
When considering the whole transcriptome analyzed by RNAseq, the differential gene expression analysis between luminal and TN/basal BCs was performed according to both IHC and PAM50 classifications. Considering the former, there were 1143 differentially expressed genes out of a total of 20936 (5.5%) and the pathways involved were “fatty acid elongation”, “cell cycle”, “oocyte meiosis”, “p53 signaling” and “alcoholism”. The analysis on the latter classification showed 1608 differentially expressed genes out of 21048 (7.6%), and the enriched pathways were “cell cycle”, “p53 signaling”, “DNA replication”, “alcoholism” and “systemic lupus erythematosus”.
Regarding the TIS, no significant differences were found between TN/basal and luminal BCs, comparing both IHC and the PAM50 subtypes. An expected heterogeneity was found among TNBCs, that showed 3 distinct signatures: basal-like immune activated, basal-like immune-suppressed and luminal androgen receptor.
Conclusions: This preliminary analysis shows a good concordance between NanoString and RNAseq data. The choice of the method must take into account important factors such as the costs, the number of genes analyzed, the requirement of bioinformatic support, the working time. Further analyses on pathway enrichment will be presented.
Table 1. Breast cancer samples characteristics.Sample ID Age Grade T N IHC subtype PAM50 Subtype TIS scoreTNBC signature 0172222aLumALumB7,0NA026031c2aTNBasal7,2BLIA037221cxTNLumA7,4LAR045231c0LumALumA7,5NA053531c1aTNBasal5,5BLIS0675320TNBasal6,2BLIS077931cxLumB HER2+LumB6,7NA0878220LumALumB7,7NA097431a2aTNBasal8,5BLIA106031c1LumB HER2+LumA8,2NA116621b0LumB HER2+LumA6,1NA1241321aTNBasal7,5BLIATIS: Tumor Inflammation Signature; BLIA: Basal-like Immune Activated; BLIS: Basal-like Immune-Suppressed; LAR: Luminal Androgen Receptor.
Citation Format: Andrea Rocca, Sara Ravaioli, Eugenio Fonzi, Iros Barozzi, Ylenia Perone, Luca Magnani, Francesca Pirini, Giovanni Martinelli, Sara Bravaccini. Breast cancer subtype classification using NanoString and RNAseq technologies [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-07-06.
Collapse
Affiliation(s)
- Andrea Rocca
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Sara Ravaioli
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Eugenio Fonzi
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Iros Barozzi
- 2Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, United Kingdom
| | - Ylenia Perone
- 2Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, United Kingdom
| | - Luca Magnani
- 2Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, United Kingdom
| | - Francesca Pirini
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Giovanni Martinelli
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Sara Bravaccini
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| |
Collapse
|
17
|
Vergara D, Ravaioli S, Fonzi E, Adamo L, Damato M, Bravaccini S, Pirini F, Gaballo A, Barbano R, Pasculli B, Franck J, Fournier I, Salzet M, Maffia M. Carbonic Anhydrase XII Expression Is Modulated during Epithelial Mesenchymal Transition and Regulated through Protein Kinase C Signaling. Int J Mol Sci 2020; 21:ijms21030715. [PMID: 31979064 PMCID: PMC7037142 DOI: 10.3390/ijms21030715] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 10/29/2019] [Revised: 01/14/2020] [Accepted: 01/20/2020] [Indexed: 01/08/2023] Open
Abstract
Members of the carbonic anhydrase family are functionally involved in the regulation of intracellular and extracellular pH in physiological and pathological conditions. Their expression is finely regulated to maintain a strict control on cellular homeostasis, and it is dependent on the activation of extracellular and intracellular signaling pathways. Combining RNA sequencing (RNA-seq), NanoString, and bioinformatics data, we demonstrated that the expression of carbonic anhydrase 12 (CAXII) is significantly different in luminal and triple negative breast cancer (BC) models and patients, and is associated with the activation of an epithelial mesenchymal transition (EMT) program. In BC models, the phorbol ester 12-myristate 13-acetate (PMA)-mediated activation of protein kinase C (PKC) induced a down-regulation of CAXII with a concomitant modulation of other members of the transport metabolon, including CAIX and the sodium bicarbonate cotransporter 3 (NBCn1). This is associated with a remodeling of tumor glycolytic metabolism induced after PKC activation. Overall, this analysis highlights the dynamic nature of transport metabolom and identifies signaling pathways finely regulating this plasticity.
Collapse
Affiliation(s)
- Daniele Vergara
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (L.A.); (M.D.)
- Laboratory of Clinical Proteomics, “Giovanni Paolo II” Hospital, 73100 ASL-Lecce, Italy
- Correspondence: (D.V.); (M.M.); Tel.: +39-0832-661915 (D.V.); +39-0832-298670 (M.M.)
| | - Sara Ravaioli
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (S.R.); (E.F.); (S.B.); (F.P.)
| | - Eugenio Fonzi
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (S.R.); (E.F.); (S.B.); (F.P.)
| | - Loredaria Adamo
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (L.A.); (M.D.)
- Laboratory of Clinical Proteomics, “Giovanni Paolo II” Hospital, 73100 ASL-Lecce, Italy
| | - Marina Damato
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (L.A.); (M.D.)
- Laboratory of Clinical Proteomics, “Giovanni Paolo II” Hospital, 73100 ASL-Lecce, Italy
| | - Sara Bravaccini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (S.R.); (E.F.); (S.B.); (F.P.)
| | - Francesca Pirini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (S.R.); (E.F.); (S.B.); (F.P.)
| | - Antonio Gaballo
- CNR-NANOTEC, Institute of Nanotechnology c/o Campus Ecotekne, 73100 Lecce, Italy;
| | - Raffaela Barbano
- Fondazione IRCCS Casa Sollievo della Sofferenza Laboratorio di Oncologia, 71013 San Giovanni Rotondo, Italy; (R.B.); (B.P.)
| | - Barbara Pasculli
- Fondazione IRCCS Casa Sollievo della Sofferenza Laboratorio di Oncologia, 71013 San Giovanni Rotondo, Italy; (R.B.); (B.P.)
| | - Julien Franck
- Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Université de Lille, INSERM, U1192 F-59000 Lille, France; (J.F.); (I.F.); (M.S.)
| | - Isabelle Fournier
- Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Université de Lille, INSERM, U1192 F-59000 Lille, France; (J.F.); (I.F.); (M.S.)
| | - Michel Salzet
- Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Université de Lille, INSERM, U1192 F-59000 Lille, France; (J.F.); (I.F.); (M.S.)
| | - Michele Maffia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (L.A.); (M.D.)
- Laboratory of Clinical Proteomics, “Giovanni Paolo II” Hospital, 73100 ASL-Lecce, Italy
- Correspondence: (D.V.); (M.M.); Tel.: +39-0832-661915 (D.V.); +39-0832-298670 (M.M.)
| |
Collapse
|
18
|
Ravaioli S, Tebaldi M, Fonzi E, Angeli D, Mazza M, Nicolini F, Lucchesi A, Fanini F, Pirini F, Tumedei MM, Cerchione C, Viale P, Sambri V, Martinelli G, Bravaccini S. ACE2 and TMPRSS2 Potential Involvement in Genetic Susceptibility to SARS-COV-2 in Cancer Patients. Cell Transplant 2020; 29:963689720968749. [PMID: 33108902 PMCID: PMC7593730 DOI: 10.1177/0963689720968749] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 09/03/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 01/11/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic. One open question is whether genetics could influence the severity of symptoms. Considering the limited data on cancer patients, we analyzed public data repositories limited to investigate angiotensin-converting enzyme 2 (ACE2) and the transmembrane serine protease 2 (TMPRSS2) expressions and genetic variants to identify the basis of individual susceptibility to SARS-CoV-2.Gene expression and variant data were retrieved from Tissue Cancer Genome Atlas, Genotype-Tissue Expression, and gnomAD. Differences in gene expression were tested with Mann-Whitney U-test. Allele frequencies of germline variants were explored in different ethnicities, with a special focus on ACE2 variants located in the binding site to SARS-CoV-2 spike protein.The analysis of ACE2 and TMPRSS2 expressions in healthy tissues showed a higher expression in the age class 20 to 59 years (false discovery rate [FDR] < 0.0001) regardless of gender. ACE2 and TMPRSS2 were more expressed in tumors from males than females (both FDR < 0.0001) and, opposite to the regulation in tissues from healthy individuals, more expressed in elderly patients (FDR = 0.005; FDR < 0.0001, respectively). ACE2 and TMPRSS2 expressions were higher in cancers of elderly patients compared with healthy individuals (FDR < 0.0001). Variants were present at low frequency (range 0% to 3%) and among those with the highest frequency, the variant S19P belongs to the SARS-CoV-2 spike protein binding site and it was exclusively present in Africans with a frequency of 0.2%.The mechanisms of ACE2 and TMPRSS2 regulation could be targeted for preventive and therapeutic purposes in the whole population and especially in cancer patients.Further studies are needed to show a direct correlation of ACE2 and TMPRSS2 expressions in cancer patients and the incidence of COVID-19.
Collapse
Affiliation(s)
- Sara Ravaioli
- Department of Clinical and Experimental oncology and hematology,
Biosciences Laboratory, Istituto
Scientifico Romagnolo per lo Studio e la Cura dei
Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Michela Tebaldi
- Department of Research and Innovation, Unit of Biostatistics and
Clinical Trials, Istituto Scientifico Romagnolo per lo
Studio e la Cura dei Tumori (IRST) IRCCS,
Meldola, FC, Italy
| | - Eugenio Fonzi
- Department of Research and Innovation, Unit of Biostatistics and
Clinical Trials, Istituto Scientifico Romagnolo per lo
Studio e la Cura dei Tumori (IRST) IRCCS,
Meldola, FC, Italy
| | - Davide Angeli
- Department of Research and Innovation, Unit of Biostatistics and
Clinical Trials, Istituto Scientifico Romagnolo per lo
Studio e la Cura dei Tumori (IRST) IRCCS,
Meldola, FC, Italy
| | - Massimiliano Mazza
- Department of Clinical and Experimental oncology and hematology,
Immunotherapy, Cell Therapy and Biobank (ITCB), Istituto
Scientifico Romagnolo per lo Studio e la Cura dei
Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Fabio Nicolini
- Department of Clinical and Experimental oncology and hematology,
Immunotherapy, Cell Therapy and Biobank (ITCB), Istituto
Scientifico Romagnolo per lo Studio e la Cura dei
Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Alessandro Lucchesi
- Department of Clinical and Experimental oncology and hematology,
Hematology Unit, Istituto Scientifico Romagnolo per lo
Studio e la Cura dei Tumori (IRST) IRCCS,
Meldola, FC, Italy
| | - Francesca Fanini
- Department of Clinical and Experimental oncology and hematology,
Biosciences Laboratory, Istituto
Scientifico Romagnolo per lo Studio e la Cura dei
Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Francesca Pirini
- Department of Clinical and Experimental oncology and hematology,
Biosciences Laboratory, Istituto
Scientifico Romagnolo per lo Studio e la Cura dei
Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Maria Maddalena Tumedei
- Department of Clinical and Experimental oncology and hematology,
Biosciences Laboratory, Istituto
Scientifico Romagnolo per lo Studio e la Cura dei
Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Claudio Cerchione
- Department of Clinical and Experimental oncology and hematology,
Hematology Unit, Istituto Scientifico Romagnolo per lo
Studio e la Cura dei Tumori (IRST) IRCCS,
Meldola, FC, Italy
| | - Pierluigi Viale
- Infectious Diseases Unit, Department of Medical and Surgical
Sciences, Alma Mater
Studiorum University of Bologna, Bologna,
Italy
| | - Vittorio Sambri
- Unit of Microbiology, The Great Romagna Area Hub Laboratory,
Pievesestina, Cesena, Italy
- Department of Experimental, Diagnostic and Specialty Medicine
(DIMES), University of Bologna, Bologna, Italy
| | - Giovanni Martinelli
- Scientific Directorate, Istituto
Scientifico Romagnolo per lo Studio e la Cura dei
Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Sara Bravaccini
- Department of Clinical and Experimental oncology and hematology,
Biosciences Laboratory, Istituto
Scientifico Romagnolo per lo Studio e la Cura dei
Tumori (IRST) IRCCS, Meldola, FC, Italy
| |
Collapse
|
19
|
Simonetti G, Padella A, Fonzi E, Pazzaglia M, Perricone M, Fontana MC, Bruno S, Bochicchio MT, Franchini E, Nanni J, Marconi G, Valle IFD, Tommaso RD, Ferrari A, Imbrogno E, Cerchione C, Papayannidis C, Ottaviani E, Remondini D, Martinelli G. Abstract 5279: Metabolic profiling defines a new characterization of acute myeloid leukemia and identifies NPM1-mutated cases as a distinct subgroup. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-5279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Genomic and functional alterations of enzymatic activity drive cancer metabolic reprogramming along with mutations of tumor suppressors and oncogenes. IDH1/2 lesions represent a paradigmatic example in acute myeloid leukemia (AML). The study aimed to stratify AML patients based on their metabolic landscape and to map potential connections between their metabolic and genomic profile. The genomic landscape of 166 AML patients was obtained by whole exome sequencing. Variants were called by MuTect and Varscan2. Six additional cases were analyzed by targeted sequencing (SOPHiA GENETICS). Metabolites were quantified by mass spectrometry of bone marrow cells (35 CD34+ and 15 CD33+ AML from the above-mentioned cohort) and compared with CD34+ cord blood and CD33+ healthy blood cells (n=21 each, Metabolon) by Welch's t-test. In AML, 17% of somatic variants targeted metabolism-related genes: 38% were enzymes (according to Recon2), including 3% of electron transport chain genes encoded by mitochondrial DNA (COX1-3, ND1-6), 3% were AML-related genes with a known involvement in cell metabolism (e.g. IDH1/2, MYC, KRAS) and 59% were metabolic regulators, defined by gene ontology annotation. Ninety-one% of patients carried at least one mutation in a metabolism-related gene, with 43% of variants rated as damaging. The most represented pathways were lipid, carbohydrate, nucleotide (AK9, H6PD), amino acids (IDO2) and glucose metabolism (PKM, HK3).
Principal component analysis of metabolic data showed a distinct profile between AML and healthy cells, with a predictive accuracy of 86% and 95% for CD34+ and CD33+ cells, respectively. Conversely, few differences were observed between CD34+ and CD33+ AML. Unsupervised hierarchical clustering clearly defined 3 AML clusters (C1-3). Moreover, 3 subgroups could be identified in C3 without ambiguous assignments. C1 was enriched for NPM1-mutated (mut) cases (83%, 33%, 27% in C1, C2 and C3, respectively, p=0.03). NPM1-mutated AML were distinguished by a 12-metabolites signature. They showed increased levels of spermidine, cytidine 2′ or 3′-monophosphate (P), thymidine 3′-monoP, uridine-2',3'-cyclic monoP and decrease of inosine 5'-monoP, suggesting altered polyamine, pyrimidine and purine metabolism. Moreover, NPM1-mut AML had reduced levels of intermediates involved in acyl carnitine, lysophospholipid, phosphatidylethanolamine and sphingolipid metabolism. Overall, mutations of metabolism-related genes are common in AML. We defined a metabolic-based classification of AML and identified a new metabolic signature based on 12 metabolites that distinguish NPM1-mut AML from wild-type cases and healthy CD34+/CD33+ cells. Major alterations in the nucleotide and polyamine pathways suggest novel potential therapeutic approaches.
Supported by: EHA research fellowship award, AIRC, FP7-NGS-PTL, Fondazione del Monte.
Citation Format: Giorgia Simonetti, Antonella Padella, Eugenio Fonzi, Martina Pazzaglia, Margherita Perricone, Maria Chiara Fontana, Samantha Bruno, Maria Teresa Bochicchio, Eugenia Franchini, Jacopo Nanni, Giovanni Marconi, Italo F. do Valle, Rossella De Tommaso, Anna Ferrari, Enrica Imbrogno, Claudio Cerchione, Cristina Papayannidis, Emanuela Ottaviani, Daniel Remondini, Giovanni Martinelli. Metabolic profiling defines a new characterization of acute myeloid leukemia and identifies NPM1-mutated cases as a distinct subgroup [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 5279.
Collapse
Affiliation(s)
- Giorgia Simonetti
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) Srl - IRCCS, Meldola (FC), Italy
| | - Antonella Padella
- 2Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Institute of Hematology "L. e A. Seràgnoli", Bologna, Italy
| | - Eugenio Fonzi
- 3Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Institute of Hematology "L. e A. Seràgnoli", Italy
| | - Martina Pazzaglia
- 3Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Institute of Hematology "L. e A. Seràgnoli", Italy
| | - Margherita Perricone
- 3Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Institute of Hematology "L. e A. Seràgnoli", Italy
| | - Maria Chiara Fontana
- 3Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Institute of Hematology "L. e A. Seràgnoli", Italy
| | - Samantha Bruno
- 3Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Institute of Hematology "L. e A. Seràgnoli", Italy
| | - Maria Teresa Bochicchio
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) Srl - IRCCS, Meldola (FC), Italy
| | - Eugenia Franchini
- 3Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Institute of Hematology "L. e A. Seràgnoli", Italy
| | - Jacopo Nanni
- 3Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Institute of Hematology "L. e A. Seràgnoli", Italy
| | - Giovanni Marconi
- 3Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Institute of Hematology "L. e A. Seràgnoli", Italy
| | | | - Rossella De Tommaso
- 3Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Institute of Hematology "L. e A. Seràgnoli", Italy
| | - Anna Ferrari
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) Srl - IRCCS, Meldola (FC), Italy
| | - Enrica Imbrogno
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) Srl - IRCCS, Meldola (FC), Italy
| | - Claudio Cerchione
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) Srl - IRCCS, Meldola (FC), Italy
| | - Cristina Papayannidis
- 3Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Institute of Hematology "L. e A. Seràgnoli", Italy
| | - Emanuela Ottaviani
- 3Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Institute of Hematology "L. e A. Seràgnoli", Italy
| | - Daniel Remondini
- 4Department of Physics and Astronomy, University of Bologna, Italy
| | - Giovanni Martinelli
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) Srl - IRCCS, Meldola (FC), Italy
| |
Collapse
|
20
|
Ferrari A, Vitali S, Robustelli V, Rorà AGLD, Fonzi E, Righi S, Baldazzi C, Tebaldi M, Salvi S, Papayannidis C, Marconi G, Fontana M, Imbrogno E, Padella A, Simonetti G, Santoro A, Hernández-Rivas JM, Bochicchio MT, Mammoli F, Giannini B, Testoni N, Calistri D, Bonafè M, Castellani G, Sabattini E, Remondini D, Martinelli G. Abstract 2140: “3c-up” a new adult Philadelphia negative acute lymphoblastic leukemia subgroup: Novel molecular markers. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-2140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The genetically heterogeneous and poor survival group of Philadelphia negative (Ph-) B-ALL group that doesn’t have the most recurrent adult rearrangements (t(9;22); t(1;19); t(4;11)) is collectively referred to as “triple negative” (Ph-/-/-). CRLF2 is frequently altered in adult B-ALL, especially in Ph-like pts (50-75% of cases). Alterations that lead, in the majority of cases, to a CRLF2 overexpression. Adult pts with CRLF2 upregulated have poor outcome and novel strategies are needed to improve it.
Aims: Understand the genomic background of all Ph-/-/- ALL and subsequently clustering Ph-/-/- considering CRLF2 overexpression event, in order to define new biomarkers in these subgroups.
Pts and Methods: Ph-/-/- pts were sequenced by WES (44pts/93 samples) and 92 B-Other pts were analyzed with NGS target seq (NTS) to validate the 8 most mutated genes (Fig1A). GEP were performed on 55 Ph-/-/-, 29 B-ALL Ph+ and on 7 donors. We cluster triple negative GEP data with our validated pipeline, based on CRLF2 upregulation and in a top ten-gene list. Ph-/-/- ALL samples were then characterized for the presence of gene fusions, Copy Number Alterations (CNAs) and mutations using different approaches (Pancancer and/or RNASeq; dMLPA-MRC-Holland; SNP Array; 454 Junior and PCR).
Results: WES analysis identified some recurrent mutated genes (NRAS, PAX5, KRAS, PTPN11, EP400, JAK2, TP53, CREBBP) previously reported to be involved in B-ALL, confirming the pivotal roles of these gene in ALL. For the first time we described a little known gene PKHD1L1 as highly mutated (7.2%). TP53 was the most mutated gene (Fig1A) and that between these gene is the only one associated to a worst OS (p=0.004). Combining our new Ph-/-/- GEP clustering, WES, NTS, Fusion and CNA results we identify a defined 2-clusters-subdivision (Gr1 and Gr2). The Gr2 (14.1% of all B-ALL) is characterized by CTGF, CRLF2 and CD200 (Gr2=3C-up; Fig 1B) co-overexpression. The Gr2 GEP is similar to Ph+ one (Fig1C). Gr1 represents 46.9% of all B-ALL. Fusion, CNA and mutational screening done, detected that 3C-Up group has a higher frequency of Ph-like associated lesions (primarily CRLF2, JAK2, IL7R mut or del), that mainly affect JAK-STAT pathway. Also IKZF1 and EBF1 deletions are significantly associated to Gr2 (p=0.003; p=0.016). RAS pathway genes are highly affected in Gr1. We also validated not previously described fusions. Notably p53 pathway is enriched in both groups but with different deregulated genes: CHEK2 is upreg in the group1 and CDK6 in the Gr2. Preliminary data seems to confirm an higher effect on cell viability of a TKI on Gr2 primary cell pt (vs Gr1 pt).
Conclusions: we identified a new signature, related to CRLF2 high expression, to classify Ph-/-/- ALL B. This new subclassification identifies new potential therapeutic targets with available drugs (α-CTGF, α-CD200, CDK2, CHK2 and CDK6 inhibitors; TKIs already effective on Ph+ and Ph-like) to test.
Citation Format: Anna Ferrari, Silvia Vitali, Valentina Robustelli, Andrea Ghelli Luserna di Rorà, Eugenio Fonzi, Simona Righi, Carmen Baldazzi, Michela Tebaldi, Samanta Salvi, Cristina Papayannidis, Giovanni Marconi, Mariachiara Fontana, Enrica Imbrogno, Antonella Padella, Giorgia Simonetti, Alessandra Santoro, Jesus María Hernández-Rivas, Maria Teresa Bochicchio, Fabiana Mammoli, Benedetta Giannini, Nicoletta Testoni, Daniele Calistri, Massimiliano Bonafè, Gastone Castellani, Elena Sabattini, Daniel Remondini, Giovanni Martinelli. “3c-up” a new adult Philadelphia negative acute lymphoblastic leukemia subgroup: Novel molecular markers [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 2140.
Collapse
Affiliation(s)
- Anna Ferrari
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | | | | | | | | | - Simona Righi
- 4Dipartimento di Medicina Specialistica Diagnostica e Sperimentale (DIMES), Bologna, Italy
| | | | - Michela Tebaldi
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Samanta Salvi
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | | | | | | | - Enrica Imbrogno
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | | | - Giorgia Simonetti
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | | | | | - Maria Teresa Bochicchio
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Fabiana Mammoli
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Benedetta Giannini
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | | | - Daniele Calistri
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Massimiliano Bonafè
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | | | - Elena Sabattini
- 4Dipartimento di Medicina Specialistica Diagnostica e Sperimentale (DIMES), Bologna, Italy
| | | | - Giovanni Martinelli
- 1Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| |
Collapse
|
21
|
Simonetti G, Padella A, do Valle IF, Fontana MC, Fonzi E, Bruno S, Baldazzi C, Guadagnuolo V, Manfrini M, Ferrari A, Paolini S, Papayannidis C, Marconi G, Franchini E, Zuffa E, Laginestra MA, Zanotti F, Astolfi A, Iacobucci I, Bernardi S, Sazzini M, Ficarra E, Hernandez JM, Vandenberghe P, Cools J, Bullinger L, Ottaviani E, Testoni N, Cavo M, Haferlach T, Castellani G, Remondini D, Martinelli G. Aneuploid acute myeloid leukemia exhibits a signature of genomic alterations in the cell cycle and protein degradation machinery. Cancer 2018; 125:712-725. [PMID: 30480765 PMCID: PMC6587451 DOI: 10.1002/cncr.31837] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/08/2018] [Accepted: 06/26/2018] [Indexed: 12/19/2022]
Abstract
Background Aneuploidy occurs in more than 20% of acute myeloid leukemia (AML) cases and correlates with an adverse prognosis. Methods To understand the molecular bases of aneuploid acute myeloid leukemia (A‐AML), this study examined the genomic profile in 42 A‐AML cases and 35 euploid acute myeloid leukemia (E‐AML) cases. Results A‐AML was characterized by increased genomic complexity based on exonic variants (an average of 26 somatic mutations per sample vs 15 for E‐AML). The integration of exome, copy number, and gene expression data revealed alterations in genes involved in DNA repair (eg, SLX4IP, RINT1, HINT1, and ATR) and the cell cycle (eg, MCM2, MCM4, MCM5, MCM7, MCM8, MCM10, UBE2C, USP37, CK2, CK3, CK4, BUB1B, NUSAP1, and E2F) in A‐AML, which was associated with a 3‐gene signature defined by PLK1 and CDC20 upregulation and RAD50 downregulation and with structural or functional silencing of the p53 transcriptional program. Moreover, A‐AML was enriched for alterations in the protein ubiquitination and degradation pathway (eg, increased levels of UHRF1 and UBE2C and decreased UBA3 expression), response to reactive oxygen species, energy metabolism, and biosynthetic processes, which may help in facing the unbalanced protein load. E‐AML was associated with BCOR/BCORL1 mutations and HOX gene overexpression. Conclusions These findings indicate that aneuploidy‐related and leukemia‐specific alterations cooperate to tolerate an abnormal chromosome number in AML, and they point to the mitotic and protein degradation machineries as potential therapeutic targets. Aneuploid acute myeloid leukemia (A‐AML) is associated with genomic and transcriptional alterations in the cell cycle and protein degradation pathways. The upregulation of PLK1 and CDC20 and the downregulation of RAD50 and of a p53‐related signature are hallmarks of A‐AML.
Collapse
Affiliation(s)
- Giorgia Simonetti
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Antonella Padella
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Italo Farìa do Valle
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy.,CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - Maria Chiara Fontana
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Eugenio Fonzi
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Samantha Bruno
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Carmen Baldazzi
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Viviana Guadagnuolo
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Marco Manfrini
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Anna Ferrari
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Stefania Paolini
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Cristina Papayannidis
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Giovanni Marconi
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Eugenia Franchini
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Elisa Zuffa
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Maria Antonella Laginestra
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Federica Zanotti
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Annalisa Astolfi
- Giorgio Prodi Cancer Research Center, University of Bologna, Bologna, Italy
| | - Ilaria Iacobucci
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Simona Bernardi
- Unit of Blood Diseases and Stem Cell Transplantation, University of Brescia, Brescia, Italy
| | - Marco Sazzini
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | | | - Jesus Maria Hernandez
- Fundación de Investigación del Cáncer de la Universidad de Salamanca, Salamanca, Spain
| | | | - Jan Cools
- Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Emanuela Ottaviani
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Nicoletta Testoni
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Michele Cavo
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | | | - Gastone Castellani
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Daniel Remondini
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Giovanni Martinelli
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| |
Collapse
|
22
|
Ferrari A, Fonzi E, Rorà AGLD, Fontana MC, Manfrini M, Baldazzi C, Papayannidis C, Solli V, Padella A, Marconi G, Paolini S, Robustelli V, Imbrogno E, Franchini E, Margherita P, Abbenante MC, Simonetti G, Testoni N, Ottaviani E, Cavo M, Martinelli G. Abstract 656: Distinct pattern of alterations in TP53 mutated/deleted and wild-type high risk acute myeloid leukemia (AML) patients: Identification of new "targetable" genes/pathways. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The reported TP53 mutation rate in AML is relatively low (7.5-9%, TCGA) and predict a poor prognosis. In 2017 European LeukemiaNet recommended for AML to add TP53 mutations (muts) in the risk stratification. Specific chromosomal aneuploidies are closely correlated with each other and with presence of TP53 muts. Aims: Considering that TP53 mut AML pts have HRisk and no target therapy, we would identify genes/pathways that are mainly CNA-affected (Copy Number Alteration) in the mut TP53 group compared to the wt one. Patients and Methods: 358 adult AML pts were screened for TP53 muts. 219/358 samples were genotyped with SNP arrays. CNA analyses were performed using two software to confirm or integrate karyotype data. Fisher's exact test and pathway enrichment analyses were performed. Results: We detected TP53 muts in 52/358 (14.5%) pts. Mostly (34/52) of the TP53 mut pts (65.4%) had complex karyotype. TP53 alterations were significantly associated with poor outcome (OS and EFS p<0.0001). On TP53 locus, we matched CNA and cytogenetic analyses results. We identify 23 mutated pts that were also deleted (alt) and 7 pts that presented only a TP53 deletion. Therefore 44.2% of mut pts present a concomitant deletion. OS of TP53 alt pts is not statistically inferior respect to mut pts (p=0.77). Comparing 52 TP53 alt and 167 TP53 wt pts CNAs results that: a) chrs significantly altered are 5q and 17p but there are also highly significant »Spot» losses (7q, 20p, 21q, 22q, 19q); b) TP53 CNAs are present in the 44% of TP53 alt vs 0.63% of wt pts; c) over 9013 genes are differentially involved (mainly in Loss, 93.1%); d) that pathway categories mainly enriched are Immune System, Metabolism, Signal Transduction; e) TP53 deletion seems less deleterious (in terms of OS) than TP53 mutation or TP53 alt; f) some TP53 protein-protein interacting genes like SKP1, CDK5, PPP2CA, CSNK1G3 and STAT5B are highly altered and drug target. Conclusions: TP53 muts with or without deletion were predicted to be deleterious and significantly correlated with worse prognosis. For these reasons, TP53 mutation/deletion screening should be recommended. Different alterations groups have been identified in terms of genes, pathway enrichment and protein-protein interaction between ALT and Wt; needed a deeper investigation to better focus on few targetable nodes of this complex network. Three groups comparison (Wt,TP53 Mut,TP53 MutDel pts) analyses would give us the opportunity to select a more appropriate target therapy in these pts. Different pattern of alterations in alt and wt groups have to be deeper investigated to discover targetable nodes of this complex network. ELN, AIL, AIRC, PRIN, Regione-Università 2010-12 (L. Bolondi), FP7 NGS-PTL; HARMONY.
Citation Format: Anna Ferrari, Eugenio Fonzi, Andrea Ghelli Luserna Di Rorà, Maria Chiara Fontana, Marco Manfrini, Carmen Baldazzi, Cristina Papayannidis, Vincenza Solli, Antonella Padella, Giovanni Marconi, Stefania Paolini, Valentina Robustelli, Enrica Imbrogno, Eugenia Franchini, Perricone Margherita, Maria Chiara Abbenante, Giorgia Simonetti, Nicoletta Testoni, Emanuela Ottaviani, Michele Cavo, Giovanni Martinelli. Distinct pattern of alterations in TP53 mutated/deleted and wild-type high risk acute myeloid leukemia (AML) patients: Identification of new "targetable" genes/pathways [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 656.
Collapse
|
23
|
Fontana MC, Marconi G, Milosevic Feenstra JD, Fonzi E, Papayannidis C, Ghelli Luserna di Rorá A, Padella A, Solli V, Franchini E, Ottaviani E, Ferrari A, Baldazzi C, Testoni N, Iacobucci I, Soverini S, Haferlach T, Guadagnuolo V, Semerad L, Doubek M, Steurer M, Racil Z, Paolini S, Manfrini M, Cavo M, Simonetti G, Kralovics R, Martinelli G. Chromothripsis in Acute Myeloid Leukemia: biological features and
impact on survival. Leukemia 2017:10.1038/leu.2017.351. [PMCID: PMC5892717 DOI: 10.1038/leu.2017.351] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
Abstract
Chromothripsis is a one-step genome-shattering catastrophe resulting from
disruption of one or few chromosomes in multiple fragments and consequent random
rejoining and repair. This study define incidence of chromothripsis in 395
newly-diagnosed adult acute myeloid leukemia (AML) patients from three
institutions, its impact on survival and its genomic background. SNP 6.0 or
CytoscanHD Array (Affymetrix®) were performed on all samples. We detected
chromothripsis with a custom algorithm in 26/395 patients. Patients harboring
chromothripsis had higher age (p=.002), ELN high risk (HR) (p<.001),
lower white blood cell (WBC) count (p=.040), TP53 loss and/or
mutations (p<.001) while FLT3 (p=.025) and
NPM1 (p=.032) mutations were mutually exclusive with
chromothripsis. Chromothripsis-positive patients showed a worse overall survival
(OS) (p<.001) compared with HR patients (p=.011) and a poor prognosis in
a COX-HR optimal regression model. Chromothripsis presented the hallmarks of
chromosome instability [i.e. TP53 alteration, 5q deletion,
higher mean of copy number alteration (CNA), complex karyotype, alterations in
DNA repair and cell cycle] and focal deletions on chromosomes 4, 7, 12, 16, 17.
CBA. FISH showed that chromothripsis is associated with marker, derivative and
ring chromosomes. In conclusion, chromothripsis frequently occurs in AML (6.6%)
and influences patient prognosis and disease biology.
Collapse
Affiliation(s)
| | - Giovanni Marconi
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | | | - Eugenio Fonzi
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | | | | | - Antonella Padella
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Vincenza Solli
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Eugenia Franchini
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Emanuela Ottaviani
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Anna Ferrari
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Carmen Baldazzi
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Nicoletta Testoni
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Ilaria Iacobucci
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Simona Soverini
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | | | | | - Lukas Semerad
- Department of Internal Medicine - Hematology and Oncology, Masaryk
University and Hospital, Brno, CR
| | - Michael Doubek
- Department of Internal Medicine - Hematology and Oncology, Masaryk
University and Hospital, Brno, CR
| | - Michael Steurer
- Division of Hematology and Oncology, Medical University of
Innsbruck, Innsbruck, Austria
| | - Zdenek Racil
- Department of Internal Medicine - Hematology and Oncology, Masaryk
University and Hospital, Brno, CR
| | - Stefania Paolini
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Marco Manfrini
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Michele Cavo
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Giorgia Simonetti
- Institute of Hematology “L. and A. Seràgnoli”,
University of Bologna, Italy
| | - Robert Kralovics
- CeMM Research Center for Molecular Medicine of the Austrian Academy
of Sciences, Wien, Austria
| | | |
Collapse
|
24
|
Fontana MC, Marconi G, Papayannidis C, Fonzi E, Simonetti G, Padella A, Ferrari A, Ottaviani E, Monaco SL, Paolini S, Soverini S, Martinelli G. Abstract 2451: Genomic wide microarray analysis identifies novel copy number alterations in adult acute myeloid leukemia. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-2451] [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
Introduction: Novel array-based technique as SNP microarray can detect losses or gains of chromosomic material, which could be predictive of response and can help define therapeutic strategies. The aim of this study is to improve conventional cytogenetic analysis and identify new genetic alterations relevant to leukemogenesis, by a SNP array-based genotyping approach.
Materials and Methods: We performed SNP 6.0 or Cytoscan HD (Affymetrix) in 235 Acute Myeloid Leukemia (AML) patients at diagnosis. Seventy-eight/235 samples were also performed by Whole Exome Sequencing, WES (HiSeq,Illumina). SNP Array data were analyzed by Nexus Copy Number v8.0 (BioDiscovery) and R Core Team.
Results: Copy Number Alterations (CNAs) were scattered across all chromosomes and all pts showed CNA events. SNP array analysis showed that several genes were preferentially deleted, including MRPS5 (14.8%), PHF6 (9.3%), SCAPER (7.2%), CASK (5.9%), WNK (4.6%), STAG2 (4.2%), LRRK1 (3.4%), PALB2 (3.4%), while the genes preferentially amplified were RABL2B (16.1%), NF2 (10.2%), NBPF9 (7.6%), JAK2 (6.8%), RB1, NF1 and KMT2A (4.2%), PTEN (3.4%), TP73 and SMAD2 (2.5%). Single-copy losses and deletions were enriched (p<.001) for genes mapping into the following pathways: aberrant PD-1 signaling, loss of function of SMAD4 in cancer and SMAD4 MH2 Domain mutants in cancer. The functional pathways significantly (p<.001) deregulated in our cohort with single copy gain and homozygous amplification were: regulation of transcription and nucleic acid, negative regulation of metabolic processes, constitutive signaling by aberrant PI3K in cancer and PI3K/AKT network. Finally, in order to define driver alterations, we correlate deletions and losses with mutational data. Interestingly, we found losses which are also targeted by mutations (BRCA2, LRRK1). Moreover, some deleted genes, as CASK, CDK6 and MAPT, were involved in pathways affected by genomic mutations (CASK deletion and MPP6 mutation, CDK6 deletion and PPM1D mutation, MAPT deletion and SPAG5 mutation).
Conclusion: We have identified new CNAs and pathways involving novel potential leukemia-related genes. Our results suggest that the comparison between SNP and WES data could provide important findings on prognosis of AML patients. Minimal deleted regions of genes implicated in deregulated pathways deserve further investigation in order to identify new candidate genes which could be relevant AML biomarkers. Acknowledgements: ELN,AIL,AIRC,progetto Regione-Università 2010-12 (L. Bolondi),FP7 NGS-PTL project,HARMONY.
Citation Format: Maria Chiara Fontana, Giovanni Marconi, Cristina Papayannidis, Eugenio Fonzi, Giorgia Simonetti, Antonella Padella, Anna Ferrari, Emanuela Ottaviani, Silvia Lo Monaco, Stefania Paolini, Simona Soverini, Giovanni Martinelli. Genomic wide microarray analysis identifies novel copy number alterations in adult acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2451. doi:10.1158/1538-7445.AM2017-2451
Collapse
Affiliation(s)
- Maria Chiara Fontana
- Department of Experimental, Diagnostic and Specialty Medicine. University of Bologna, Bologna, Italy
| | - Giovanni Marconi
- Department of Experimental, Diagnostic and Specialty Medicine. University of Bologna, Bologna, Italy
| | - Cristina Papayannidis
- Department of Experimental, Diagnostic and Specialty Medicine. University of Bologna, Bologna, Italy
| | - Eugenio Fonzi
- Department of Experimental, Diagnostic and Specialty Medicine. University of Bologna, Bologna, Italy
| | - Giorgia Simonetti
- Department of Experimental, Diagnostic and Specialty Medicine. University of Bologna, Bologna, Italy
| | - Antonella Padella
- Department of Experimental, Diagnostic and Specialty Medicine. University of Bologna, Bologna, Italy
| | - Anna Ferrari
- Department of Experimental, Diagnostic and Specialty Medicine. University of Bologna, Bologna, Italy
| | - Emanuela Ottaviani
- Department of Experimental, Diagnostic and Specialty Medicine. University of Bologna, Bologna, Italy
| | - Silvia Lo Monaco
- Department of Experimental, Diagnostic and Specialty Medicine. University of Bologna, Bologna, Italy
| | - Stefania Paolini
- Department of Experimental, Diagnostic and Specialty Medicine. University of Bologna, Bologna, Italy
| | - Simona Soverini
- Department of Experimental, Diagnostic and Specialty Medicine. University of Bologna, Bologna, Italy
| | - Giovanni Martinelli
- Department of Experimental, Diagnostic and Specialty Medicine. University of Bologna, Bologna, Italy
| |
Collapse
|
25
|
Ferrari A, Fonzi E, Fontana MC, Rorà AGLD, Manfrini M, Padella A, Baldazzi C, Papayannidis C, Marconi G, Paolini S, Guadagnuolo V, Perricone M, Robustelli V, Imbrogno E, Franchini E, Venturi C, Zuffa E, Abbenante MC, Simonetti G, Testoni N, Ottaviani E, Giovanni M. Abstract 1766: Distinct pattern of alterations in tp53 mutated and wild type acute myeloid leukemia (AML) patients. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Mutations in TP53 gene predict a poor prognosis in patients with AML. The reported TP53 mutation rate in AML is low (2.1%) by contrast AML with a complex karyotype (CK) is higher (69-78%) and have a poor outcome. Quite common is to found paired TP53 mutation together and a segmental 17p deletion.
Aims: To investigate the frequency, the types of mutations, the associated cytogenetic, the correlation with known molecular alterations and the prognostic role TP53 mutations in adult AML pts. Moreover we would identify genes/pathways that are mainly affected in the mutated TP53 group compared to the wt one.
Patients and Methods: 258 adult AML pts with miscellaneous cytogenetic abnormalities and normal karyotype were examined in our Institution for TP53 mutations using several methods, including Sanger sequencing, NGS and HiSeq2000 platform and were correlated with cytogenetic analysis. 124/258 samples were genotyped with SNP arrays (Affymetrix, 3 250K, 43 SNP 6.0, 78 CytoScan HD). Copy Number Alterations (CNAs) analyses were performed using Chromosome Analysis Suite (Affymetrix) and Nexus Copy Number (BioDiscovery) software.
Results: Mutation analysis detected TP53 mutations on 39 patients with 48 different types of mutations (32 deleterious point mutations; 4 deletions); nine pts have 2 mutations. We found 34/48 (70%) missense mutations, 5 mutations in the splice sites, 4 deletions ,2 intronic and and 3 others mutations. The mutation rate is of 15.1%. Mostly (28/39) of the TP53 mutated pts (71.8%) had CK while only 11/39 (28.2%) mutated pts have “no CK” (P>0.0001). Alterations of TP53 were significantly associated with poor outcome (OS and EFS p<0.0001). To take advantage of different methodological characteristics, on TP53 locus, we matched two software and cytogenetic analysis results. We identify 16 mutated pts that were also deleted and one pt that presented only a deletion. Therefore 50% of mutated pts present a concomitant deletion. OS of TP53 mutated and deleted pts is statistically inferior respect to muted pts (p<0.0061). Comparing 32 TP53 mutated and 92 TP53 wt pts CNAs results that: a) chromosomes significantly alterated are 5q, 17p, 12p, 16q, 22q13.33 and 7q; b) over 900 genes are differentially involved (all in Loss); c) and that pathway categories mainly enriched are Signal Transduction, Metabolism, Immune System, Transmembrane transport of small molecules, Gene expression, Cell Cycle.
Conclusions: Our data demonstrated that TP53 mutations occur in 15.1% of AML with a higher frequency in the subgroup of CK-AML (p<0.0001). They predicted to be deleterious and significantly correlated with worse prognosis especially if TP53 is both mutated and also deleted. For these reasons, TP53 mutation/deletion screening should be recommended. Different pattern of alterations in mutated and wt groups have to be deeper investigated. ELN, AIL, AIRC, progetto Regione-Università 2010-12 (L. Bolondi), FP7 NGS-PTL project.
Citation Format: Anna Ferrari, Eugenio Fonzi, Maria Chiara Fontana, Andrea Ghelli Luserna Di Rorà, Marco Manfrini, Antonella Padella, Carmen Baldazzi, Cristina Papayannidis, Giovanni Marconi, Stefania Paolini, Viviana Guadagnuolo, Margherita Perricone, Valentina Robustelli, Enrica Imbrogno, Eugenia Franchini, Claudia Venturi, Elisa Zuffa, Maria Chiara Abbenante, Giorgia Simonetti, Nicoletta Testoni, Emanuela Ottaviani, Martinelli Giovanni. Distinct pattern of alterations in tp53 mutated and wild type acute myeloid leukemia (AML) patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1766. doi:10.1158/1538-7445.AM2017-1766
Collapse
|
26
|
Lo Monaco S, Marconi G, Fontana MC, Papayannidis C, Fonzi E, Baldazzi C, Testoni N, Ottaviani E, Franchini E, Ferrari A, Simonetti G, Padella A, Ghelli Luserna di Rorà A, Robustelli V, Paolini S, Abbenante MC, Parisi S, Nanni J, Bertamini L, Martinelli G. Deficient necroptosis pathway as a negative prognostic factor in acute myeloid leukemia. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.11611] [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
11611 Background: Necroptosis is a type of necrotic cell death involving several genes transcription and activation of molecular mechanisms as death receptors, interferon, toll-like receptors, intracellular RNA and DNA sensors.The process is leading by the family of receptor-interacting protein kinase ( RIPK3, RIPK2, RIPK1) and the MLKL substrate. Losses of RIPK3 or MLKL, as well as deficiency in apoptosis, could allow tumor cells to escape the immunomediated cells death (ICD). Methods: We performed SNP Arrays (Cytoscan HD and SNP 6.0, Affymetrix) on a cohort of 300 non-M3 AML patients at diagnosis and we analyzed the Overall Survival (OS) of our patients with deficiency on necroptosis pathways. Survival was analyzed with Kaplan-Mayer method and Log-Rank test. We further analyze the relevance of different prognostic factors by the use of COX-Hazard Ratio statistical analysis. Results: We find that 18 patients presented a loss of RIPK1 or MLKL (nobody presented losses in RIPK3/RIPK2) and 13/18 patients were older than 65 years old. The Overall Survival (OS) of patients with alterations in these genes is significantly lower than control group, with a median OS of 3 vs 6 month respectively (p<.0.001). With Fisher Exact Test we further demonstrate that copy number loss of RIPK1 or MLKL are associate to loss of TP53 or FANCAgenes, complex karyotype and advanced age. COXHR model with RIPK1 or MLKL loss, BRACA1 loss, TP53 mutation, FANCA loss, secondary disease and diagnosis karyotype considered as categorical variable shows that necroptosis deficiency (HR 1.98, CI 95% 1.04-3.78), TP53mutation , and secondary AML are independent negative prognostic factors in an optimal model. Conclusions: Our study shows that losses in necroptosis pathways are an uncommon alteration in AML, prevalent in old population. Moreover, we hypothesize that the loss of genes involved in necroptosis could be a real mechanism of tumor immune-escape and could be a rational to select patients that have high probability to be resistant at chemotherapy promoting ICD mechanism. Acknowledgment: ELN,AIL,AIRC, progetto Regione-Università 2010-12, FP7 NGS-PTL project,HARMONY.
Collapse
Affiliation(s)
| | - Giovanni Marconi
- Istituto Seragnoli, DIMES, University of Bologna, Bologna, Italy
| | | | | | | | | | - Nicoletta Testoni
- Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | - Emanuela Ottaviani
- Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | | | | | - Giorgia Simonetti
- Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | | | | | | | | | | | | | - Jacopo Nanni
- University of Bologna, School of Medicine, Bologna, Italy
| | | | - Giovanni Martinelli
- Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| |
Collapse
|
27
|
Fontana MC, Marconi G, Papayannidis C, Fonzi E, Ottaviani E, Franchini E, Ferrari A, Simonetti G, Padella A, Bruno S, Testoni N, Baldazzi C, Ghelli Luserna di Rorà A, Robustelli V, Abbenante MC, Paolini S, Nanni J, Bertamini L, Martinelli G. Microarray analysis to identifiy novel copy number alterations in acute myeloid leukemia. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.11622] [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
11622 Background: SNP microarray can detect Copy Number Alterations (CNAs) which could be predictive of response and can help define therapeutic strategies. Our aim is to improve conventional cytogenetic analysis and identify new genetic alterations relevant to leukemogenesis by a SNP array-based genotyping approach. Methods: We performed SNP 6.0/Cytoscan HD (Affymetrix) on 235 Acute Myeloid Leukemia (AML) patients at diagnosis. Seventy-eight/235 samples were also performed by Whole Exome Sequencing, WES (HiSeq,Illumina). SNP Array data were analyzed by Nexus Copy Number (BioDiscovery) and R Core Team. Results: We found several genes preferentially deleted, including MRPS5 (14.8%), PHF6 (9.3%), SCAPER (7.2%), CASK (5.9%), WNK (4.6%), STAG2 (4.2%), LRRK1 (3.4%), PALB2 (3.4%), genes preferentially amplified were RABL2B (16.1%), NF2 (10.2%), NBPF9 (7.6%), JAK2 (6.8%), RB1, NF1 and KMT2A (4.2%), PTEN (3.4%), TP73 and SMAD2 (2.5%). Single-copy losses and deletions were enriched (p < .001) for genes mapping in these pathways: aberrant PD-1 signaling, loss of function of SMAD4 in cancer and SMAD4 MH2 Domain mutants in cancer. The pathways significantly (p < .001) deregulated in our cohort with single copy gain and homozygous amplification were: regulation of transcription and nucleic acid, negative regulation of metabolic processes, constitutive signaling by aberrant PI3K in cancer and PI3K/AKT network. In order to define driver alterations, we correlate deletions and losses with mutational data. We found losses are also targeted by mutations ( BRCA2, LRRK1), while deleted genes, as CASK, CDK6 and MAPT, were involved in pathways affected by genomic mutations ( CASK deletion and MPP6 mutation, CDK6 deletion and PPM1D mutation, MAPT deletion and SPAG5mutation). Conclusions: We have identified new CNAs and pathways involving novel potential leukemia-related genes. The comparison between SNP and WES data could provide important findings on prognosis of AML patients. Minimal deleted regions of genes in deregulated pathways deserve further investigation in order to identify new genes which could be relevant AML biomarkers. Ackn: ELN, AIL, AIRC,prog. Regione-Università 2010-12 (L. Bolondi),FP7 NGS-PTL project,HARMONY.
Collapse
Affiliation(s)
| | | | | | | | - Emanuela Ottaviani
- Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | | | | | - Giorgia Simonetti
- Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | | | | | - Nicoletta Testoni
- Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | | | | | | | | | | | - Jacopo Nanni
- University of Bologna, School of Medicine, Bologna, Italy
| | | | - Giovanni Martinelli
- Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| |
Collapse
|
28
|
Marconi G, Fontana MC, Papayannidis C, Padella A, Lo Monaco S, Abbenante MC, Sartor C, Bertamini L, Nanni J, Ghelli Luserna di Rorà A, Robustelli V, Tenti E, Tenti E, Fonzi E, Simonetti G, Ottaviani E, Baldazzi C, Testoni N, Martinelli G. Prognostic significance of alterations of pathways regulating autophagy in acute myeloid leukemia. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.7038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
7038 Background: Nowadays, science is debating if autophagy in cancer can lead to therapy resistance or it can favor apoptosis. Autophagy pathways are involved pro-apoptotic mechanism, or they can improve stresses survival eliminating damaged mitochondria and proteins. Levels and activity of pro-apoptotic and anti-apoptotic proteins (eg. bcl-2 and p53), high levels of cAMP, and a pink/park complex could play as fulcrum on this lever. Our study aims to define the role of autophagy in AML. Methods: We analyzed 148 consecutive non M3 AML with Affymetrix SNP array. We screened all patients for TP53, FLT3, NMP1 mutations. Patients was treated with intensive induction chemotherapy regimens. Survival data were collected prospectively, with a median follow-up of 18 months. Results: Autophagy alteration (gene group 1: ULK1 CHR11; ULK1 CHR17; BECN1; ATG14; AMBRA1; UVRAG; ATG9A; ATG9B; PIK3C3; PIK3R4) was related to lower Complete Remission rate (CR%) after induction in univariate (p < .001) and multivariable regression model with age, karyotype, secondary AML, TP53 mutation (p = .014); autophagy alteration shown to confer worst Overal Survival (OS) (p < .001) and was significantly associated with complex karyotype and TP53 mutation (p < .001). We detected significant differences in term of survival independently both in gain and loss in group 1 genes (p < .001). Alterations in genes in cAMP pathway (group 2: SESN1; PRKAA1 CHR 3; PRKAB1: PRKAA1 CHR 1: PRKAG1 CHR11; PRKAG1 CHR 7; PRKAG3; PRKAB1) and in genes that could be related to a switch from a physiological role of autophagy to a resiliency mechanism (group 3: CCND1; BCL2; PINK1; PARK2; TP53; MDM1; MDM4) showed to confer worst OS (p < .001 in both groups); Alteration in group 2 and group 3 were related to lower CR% after induction (p < .001 in both groups). Whole Exome Sequencing on 56 patients in our set did not found any significant mutation in genes we analyzed with the exception of TP53. Conclusions: Alterations in autophagy regulator genes are associated with poor prognosis and therapy resistance. A loss in autophagy could block apoptosis, a gain could confer cell resiliency. Acknowledgements: ELN, AIL, AIRC, Progetto Regione-Università 2010-12,FP7 NGS-PTL, HARMONY
Collapse
Affiliation(s)
- Giovanni Marconi
- Istituto Seragnoli, DIMES, University of Bologna, Bologna, Italy
| | | | | | | | | | | | | | | | - Jacopo Nanni
- University of Bologna, School of Medicine, Bologna, Italy
| | | | | | - Elena Tenti
- IRCCS - IRST (Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori), Meldola, Italy
| | - Elena Tenti
- Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | | | - Giorgia Simonetti
- Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | - Emanuela Ottaviani
- Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | | | - Nicoletta Testoni
- Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | - Giovanni Martinelli
- Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| |
Collapse
|
29
|
Fonzi E, Higa Y, Bertuso AG, Futami K, Minakawa N. Human-Mediated Marine Dispersal Influences the Population Structure of Aedes aegypti in the Philippine Archipelago. PLoS Negl Trop Dis 2015; 9:e0003829. [PMID: 26039311 PMCID: PMC4454683 DOI: 10.1371/journal.pntd.0003829] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/14/2015] [Indexed: 11/22/2022] Open
Abstract
Background Dengue virus (DENV) is an extraordinary health burden on global scale, but still lacks effective vaccine. The Philippines is endemic for dengue fever, but massive employment of insecticides favored the development of resistance mutations in its major vector, Aedes aegypti. Alternative vector control strategies consist in releasing artificially modified mosquitos in the wild, but knowledge on their dispersal ability is necessary for a successful implementation. Despite being documented that Ae. aegypti can be passively transported for long distances, no study to date has been aimed at understanding whether human marine transportation can substantially shape the migration patterns of this mosquito. With thousands of islands connected by a dense network of ships, the Philippines is an ideal environment to fill this knowledge gap. Methodology/principal findings Larvae of Ae. aegypti from 15 seaports in seven major islands of central-western Philippines were collected and genotyped at seven microsatellite loci. Low genetic structure and considerable gene flow was found in the area. Univariate and multivariate regression analyses suggested that anthropic factors (specifically the amount of processed cargo and human population density) can explain the observed population structure, while geographical distance was not correlated. Interestingly, cargo shipments seem to be more efficient than passenger ships in transporting Ae. aegypti. Bayesian clustering confirmed that Ae. aegypti from busy ports are more genetically similar, while populations from idle ports are relatively structured, regardless of the geographical distance that separates them. Conclusions/significance The results confirmed the pivotal role of marine human-mediated long-range dispersal in determining the population structure of Ae. aegypti. Hopefully corroborated by further research, the present findings could assist the design of more effective vector control strategies. Dengue fever threatens the health of millions in the tropics and its causative agent, dengue virus, is mainly transmitted by the mosquito Aedes aegypti. To control the spread of the virus, insecticides have been abundantly used but Ae. aegypti has developed a genetic resistance to them. Currently, alternative methods are being tested wherein artificially modified mosquitos are released in the wild to interfere with the mating of natural populations. It is important then to understand how the mosquito spreads in the environment. It is known that Ae. aegytpi can be passively transported for long distances by human vehicles, but it was not clear how common this event is, especially in case of marine transportation. In population genetics, a basic assumption says that if populations frequently exchange migrants, they become genetically more similar than relatively isolated populations. We estimated the genetic similarity between Ae. aegypti collected in the Philippines from 15 seaports of different sizes and ship connectivity. The mosquitos from busy ports, even distant ones, were genetically similar, while in the small ports, even close ones, Ae. aegypti were relatively differentiated. It was also suggested that Ae. aegypti's dispersal is affected by cargo shipments more than passenger ships.
Collapse
Affiliation(s)
- Eugenio Fonzi
- Department of Vector Ecology and Environment, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- * E-mail:
| | - Yukiko Higa
- Department of Vector Ecology and Environment, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Arlene G. Bertuso
- Department of Public Health, University of the Philippines, Manila, Philippines
| | - Kyoko Futami
- Department of Vector Ecology and Environment, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Noboru Minakawa
- Department of Vector Ecology and Environment, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| |
Collapse
|