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Zammarchi F, Havenith KE, Sachini N, Janghra N, Chivers S, Idusogie E, Gaudio E, Tarantelli C, Bertelli F, Santos K, Tyrer P, Corbett S, Spriano F, Golino G, Cascione L, Bertoni F, Hartley JA, van Berkel PH. ADCT-602, a Novel PBD Dimer-containing Antibody-Drug Conjugate for Treating CD22-positive Hematologic Malignancies. Mol Cancer Ther 2024; 23:520-531. [PMID: 38324336 PMCID: PMC10985467 DOI: 10.1158/1535-7163.mct-23-0506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/22/2023] [Accepted: 01/16/2024] [Indexed: 02/08/2024]
Abstract
Relapsed or refractory B-cell acute lymphoblastic leukemia (R/R B-ALL) and lymphomas have poor patient outcomes; novel therapies are needed. CD22 is an attractive target for antibody-drug conjugates (ADCs), being highly expressed in R/R B-ALL with rapid internalization kinetics. ADCT-602 is a novel CD22-targeting ADC, consisting of humanized mAb hLL2-C220, site specifically conjugated to the pyrrolobenzodiazepine dimer-based payload tesirine. In preclinical studies, ADCT-602 demonstrated potent, specific cytotoxicity in CD22-positive lymphomas and leukemias. ADCT-602 was specifically bound, internalized, and trafficked to lysosomes in CD22-positive tumor cells; after cytotoxin release, DNA interstrand crosslink formation persisted for 48 hours. In the presence of CD22-positive tumor cells, ADCT-602 caused bystander killing of CD22-negative tumor cells. A single ADCT-602 dose led to potent, dose-dependent, in vivo antitumor activity in subcutaneous and disseminated human lymphoma/leukemia models. Pharmacokinetic analyses (rat and cynomolgus monkey) showed excellent stability and tolerability of ADCT-602. Cynomolgus monkey B cells were efficiently depleted from circulation after one dose. Gene signature association analysis revealed IRAK1 as a potential marker for ADCT-602 resistance. Combining ADCT-602 + pacritinib was beneficial in ADCT-602-resistant cells. Chidamide increased CD22 expression on B-cell tumor surfaces, increasing ADCT-602 activity. These data support clinical testing of ADCT-602 in R/R B-ALL (NCT03698552) and CD22-positive hematologic cancers.
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Affiliation(s)
| | | | | | | | | | - Esohe Idusogie
- ADC Therapeutics America, Inc, Murray Hill, United States
| | - Eugenio Gaudio
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Chiara Tarantelli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | | | | | - Peter Tyrer
- AstraZeneca (MedImmune/Spirogen), London, United Kingdom
| | | | - Filippo Spriano
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Gaetanina Golino
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
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2
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Arribas AJ, Napoli S, Cascione L, Barnabei L, Sartori G, Cannas E, Gaudio E, Tarantelli C, Mensah AA, Spriano F, Zucchetto A, Rossi FM, Rinaldi A, Castro de Moura M, Jovic S, Bordone Pittau R, Stathis A, Stussi G, Gattei V, Brown JR, Esteller M, Zucca E, Rossi D, Bertoni F. ERBB4-Mediated Signaling Is a Mediator of Resistance to PI3K and BTK Inhibitors in B-cell Lymphoid Neoplasms. Mol Cancer Ther 2024; 23:368-380. [PMID: 38052765 DOI: 10.1158/1535-7163.mct-23-0068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/28/2023] [Accepted: 10/11/2023] [Indexed: 12/07/2023]
Abstract
BTK and PI3K inhibitors are among the drugs approved for the treatment of patients with lymphoid neoplasms. Although active, their ability to lead to long-lasting complete remission is rather limited, especially in the lymphoma setting. This indicates that tumor cells often develop resistance to the drugs. We started from a marginal zone lymphoma cell line, Karpas-1718, kept under prolonged exposure to the PI3Kδ inhibitor idelalisib until acquisition of resistance, or with no drug. Cells underwent transcriptome, miRNA and methylation profiling, whole-exome sequencing, and pharmacologic screening, which led to the identification of the overexpression of ERBB4 and its ligands HBEGF and NRG2 in the resistant cells. Cellular and genetic experiments demonstrated the involvement of this axis in blocking the antitumor activity of various BTK/PI3K inhibitors, currently used in the clinical setting. Addition of recombinant HBEGF induced resistance to BTK/PI3K inhibitors in parental cells and in additional lymphoma models. Combination with the ERBB inhibitor lapatinib was beneficial in resistant cells and in other lymphoma models already expressing the identified resistance factors. An epigenetic reprogramming sustained the expression of the resistance-related factors, and pretreatment with demethylating agents or EZH2 inhibitors overcame the resistance. Resistance factors were also shown to be expressed in clinical specimens. In conclusion, we showed that the overexpression of ERBB4 and its ligands represents a novel mechanism of resistance for lymphoma cells to bypass the antitumor activity of BTK and PI3K inhibitors and that targeted pharmacologic interventions can restore sensitivity to the small molecules.
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Affiliation(s)
- Alberto J Arribas
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sara Napoli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Laura Barnabei
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Giulio Sartori
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Eleonora Cannas
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Eugenio Gaudio
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Chiara Tarantelli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Afua A Mensah
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Filippo Spriano
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | | | | | - Andrea Rinaldi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Manuel Castro de Moura
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Sandra Jovic
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | | | - Anastasios Stathis
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Georg Stussi
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Valter Gattei
- Centro di Riferimento Oncologico di Aviano - CRO, Aviano, Italy
| | - Jennifer R Brown
- Chronic Lymphocytic Leukemia Center, Division of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Emanuele Zucca
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Davide Rossi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
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3
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Hedayat S, Cascione L, Cunningham D, Schirripa M, Lampis A, Hahne JC, Tunariu N, Hong SP, Marchetti S, Khan K, Fontana E, Angerilli V, Delrieux M, Nava Rodrigues D, Procaccio L, Rao S, Watkins D, Starling N, Chau I, Braconi C, Fotiadis N, Begum R, Guppy N, Howell L, Valenti M, Cribbes S, Kolozsvari B, Kirkin V, Lonardi S, Ghidini M, Passalacqua R, Elghadi R, Magnani L, Pinato DJ, Di Maggio F, Ghelardi F, Sottotetti E, Vetere G, Ciraci P, Vlachogiannis G, Pietrantonio F, Cremolini C, Cortellini A, Loupakis F, Fassan M, Valeri N. Circulating microRNA analysis in a prospective co-clinical trial identifies MIR652-3p as a response biomarker and driver of regorafenib resistance mechanisms in colorectal cancer. Clin Cancer Res 2024:734699. [PMID: 38376926 DOI: 10.1158/1078-0432.ccr-23-2748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND The multi-kinase inhibitor regorafenib has demonstrated efficacy in chemo-refractory metastatic colorectal cancer (mCRC) patients. However, lack of predictive biomarkers and concerns over significant toxicities hamper the use of regorafenib in clinical practice. METHODS Serial liquid biopsies were obtained at baseline and monthly until disease progression in chemo-refractory mCRC patients treated with regorafenib in a phase II clinical trial (PROSPECT-R n=40; NCT03010722) and in a multicentric validation cohort (n=241). Tissue biopsies collected at baseline, after 2 months and at progression in the PROSPECT-R trial were used to establish Patient-Derived Organoids (PDOs) and for molecular analyses. MicroRNA profiling was performed on baseline bloods using the NanoString nCounter platform and results were validated by digital droplet PCR and/or In Situ Hybridization in paired liquid and tissue biopsies. PDOs co-cultures and PDO-xenotransplants were generated for functional analyses. RESULTS Large-scale microRNA expression analysis in longitudinal matched liquid and tissue biopsies from the PROSPECT-R trial identified MIR652-3p as a biomarker of clinical benefit to regorafenib. These findings were confirmed in an independent validation cohort and in a "control" group of 100 patients treated with lonsurf. Using ex vivo co-culture assays paired with single-cell RNA-sequencing of PDO established pre- and post-treatment, we modelled regorafenib response observed in vivo and in patients, and showed that MIR652-3p controls resistance to regorafenib by impairing regorafenib-induced lethal autophagy and by orchestrating the switch from neo-angiogenesis to vessel co-option. CONCLUSIONS Our results identify MIR652-3p as potential biomarker and as a driver of cell and non-cell autonomous mechanisms of resistance to regorafenib.
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Affiliation(s)
| | - Luciano Cascione
- IOR - Institute of Oncology Research, Bellinzona, Ticino, Switzerland
| | | | - Marta Schirripa
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States
| | - Andrea Lampis
- Institute of Cancer Research, Sutton, United Kingdom
| | - Jens C Hahne
- Institute of Cancer Research, Sutton, United Kingdom
| | | | - Sung Pil Hong
- Yonsei University College of Medicine, Seoul, Korea (South), Republic of
| | | | - Khurum Khan
- Institute of Cancer Research, Sutton, United Kingdom
| | - Elisa Fontana
- Sarah Cannon Research Institute, London, London, United Kingdom
| | | | - Mia Delrieux
- Institute of Cancer Research, Sutton, United Kingdom
| | | | | | - Sheela Rao
- Royal Marsden NHS Foundation Trust, Sutton, Surrey, United Kingdom
| | | | | | - Ian Chau
- Royal Marsden Hospital, Sutton, Surrey, United Kingdom
| | | | | | - Ruwaida Begum
- Royal Marsden NHS Foundation Trust, London and Surrey, United Kingdom
| | - Naomi Guppy
- Institute of Cancer Research, London, United Kingdom
| | - Louise Howell
- Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | | | | | | | | | - Sara Lonardi
- Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
| | | | | | | | - Luca Magnani
- Institute of Cancer Research, London, United Kingdom
| | | | | | | | | | | | - Paolo Ciraci
- Azienda Ospedaliera Universitaria Pisana, Pisa, Italy
| | | | | | | | | | | | | | - Nicola Valeri
- Institute of Cancer Research, Sutton, London, United Kingdom
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4
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Sartori G, Tarantelli C, Spriano F, Gaudio E, Cascione L, Mascia M, Barreca M, Arribas AJ, Licenziato L, Golino G, Ferragamo A, Pileri S, Damia G, Zucca E, Stathis A, Politz O, Wengner AM, Bertoni F. The ATR inhibitor elimusertib exhibits anti-lymphoma activity and synergizes with the PI3K inhibitor copanlisib. Br J Haematol 2024; 204:191-205. [PMID: 38011941 DOI: 10.1111/bjh.19218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/29/2023]
Abstract
The DNA damage response (DDR) is the cellular process of preserving an intact genome and is often deregulated in lymphoma cells. The ataxia telangiectasia and Rad3-related (ATR) kinase is a crucial factor of DDR in the response to DNA single-strand breaks. ATR inhibitors are agents that have shown considerable clinical potential in this context. We characterized the activity of the ATR inhibitor elimusertib (BAY 1895344) in a large panel of lymphoma cell lines. Furthermore, we evaluated its activity combined with the clinically approved PI3K inhibitor copanlisib in vitro and in vivo. Elimusertib exhibits potent anti-tumour activity across various lymphoma subtypes, which is associated with the expression of genes related to replication stress, cell cycle regulation and, as also sustained by CRISPR Cas9 experiments, CDKN2A loss. In several tumour models, elimusertib demonstrated widespread anti-tumour activity stronger than ceralasertib, another ATR inhibitor. This activity is present in both DDR-proficient and DDR-deficient lymphoma models. Furthermore, a combination of ATR and PI3K inhibition by treatment with elimusertib and copanlisib has in vitro and in vivo anti-tumour activity, providing a potential new treatment option for lymphoma patients.
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Affiliation(s)
- Giulio Sartori
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Chiara Tarantelli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Filippo Spriano
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Eugenio Gaudio
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michele Mascia
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Marilia Barreca
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Alberto J Arribas
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Luca Licenziato
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Department of Veterinary Sciences, University of Turin, Turin, Italy
| | - Gaetanina Golino
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Adele Ferragamo
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Stefano Pileri
- Division of Diagnostic Haematopathology, European Institute of Oncology, Milan, Italy
| | - Giovanna Damia
- Laboratory of Molecular Pharmacology, Department of Oncology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Milan, Italy
| | - Emanuele Zucca
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, EOC, Bellinzona, Switzerland
| | - Anastasios Stathis
- Oncology Institute of Southern Switzerland, EOC, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, USI, Lugano, Switzerland
| | - Oliver Politz
- Bayer AG, Pharmaceuticals, Research & Development, Berlin, Germany
| | - Antje M Wengner
- Bayer AG, Pharmaceuticals, Research & Development, Berlin, Germany
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, EOC, Bellinzona, Switzerland
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5
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Arribas AJ, Gaudio E, Napoli S, Yvon Herbaux CJ, Tarantelli C, Bordone RP, Cascione L, Munz N, Aresu L, Sgrignani J, Rinaldi A, Kwee I, Rossi D, Cavalli A, Zucca E, Stussi G, Stathis A, Sloss C, Davids MS, Bertoni F. PI3Kδ activation, IL6 over-expression, and CD37 loss cause resistance to the targeting of CD37-positive lymphomas with the antibody-drug conjugate naratuximab emtansine. bioRxiv 2023:2023.11.14.566994. [PMID: 38014209 PMCID: PMC10680772 DOI: 10.1101/2023.11.14.566994] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Purpose The transmembrane protein CD37 is expressed almost exclusively in lymphoid tissues, with the highest abundance in mature B cells. CD37-directed antibody- and, more recently, cellular-based approaches have shown preclinical and promising early clinical activity. Naratuximab emtansine (Debio 1562, IMGN529) is an antibodydrug conjugate (ADC) that incorporates an anti-CD37 monoclonal antibody conjugated to the maytansinoid DM1 as payload. Naratuximab emtansine has shown activity as a single agent and in combination with the anti-CD20 monoclonal antibody rituximab in B cell lymphoma patients. Experimental Design We assessed the activity of naratuximab emtansine using in vitro models of lymphomas, correlated its activity with CD37 expression levels, characterized two resistance mechanisms to the ADC, and identified combination partners providing synergy. Results The anti-tumor activity of naratuximab emtansine was tested in 54 lymphoma cell lines alongside its free payload. The median IC 50 of naratuximab emtansine was 780 pM, and the activity, primarily cytotoxic, was more potent in B than in T cell lymphoma cell lines. In the subgroup of cell lines derived from B cell lymphoma, there was some correlation between sensitivity to DM1 and sensitivity to naratuximab emtansine (r=0.28, P = 0.06). After prolonged exposure to the ADC, one diffuse large B cell lymphoma (DLBCL) cell line developed resistance to the ADC due to the biallelic loss of the CD37 gene. After CD37 loss, we also observed upregulation of IL6 (IL-6) and other transcripts from MYD88/IL6-signaling. Recombinant IL6 led to resistance to naratuximab emtansine, while the anti-IL6 antibody tocilizumab improved the cytotoxic activity of the ADC in CD37-positive cells. In a second model, resistance was sustained by an activating mutation in the PIK3CD gene, associated with increased sensitivity to PI3K δ inhibition and a switch from functional dependence on the anti-apoptotic protein MCL1 to reliance on BCL2. The addition of idelalisib or venetoclax to naratuximab emtansine overcame resistance to the ADC in the resistant derivative while also improving the cytotoxic activity of the ADC in the parental cells. Conclusions Targeting B cell lymphoma with the CD37 targeting ADC naratuximab emtansine showed vigorous anti-tumor activity as a single agent, which was also observed in models bearing genetic lesions associated with inferior outcomes, such as MYC translocations and TP53 inactivation or resistance to R-CHOP. Resistance DLBCL models identified active combinations of naratuximab emtansine with drugs targeting IL6, PI3K δ , and BCL2. Despite notable progress in recent decades, we still face challenges in achieving a cure for a substantial number of lymphoma patients (1,2). A pertinent example is diffuse large B cell lymphoma (DLBCL), the most prevalent type of lymphoma (3). More than half of DLBCL patients can achieve remission, but around 40% of them experience refractory disease or relapse following an initial positive response (3). Regrettably, the prognosis for many of these cases remains unsatisfactory despite introducing the most recent antibody-based or cellular therapies (3,4), underscoring the importance of innovating new therapeutic strategies and gaining insights into the mechanisms of therapy resistance. CD37 is a transmembrane glycoprotein belonging to the tetraspanin family, primarily expressed on the surface of immune cells, principally in mature B cells but also, at lower levels, in T cells, macrophages/monocytes, granulocytes and dendritic cells (5) (6-8). CD37 plays a crucial role in various immune functions, including B cell activation, proliferation, and signaling, although its precise role still needs to be fully elucidated. CD37 interacts with multiple molecules, including SYK, LYN, CD19, CD22, PI3K δ , PI3K γ , and different integrins, among others (6-8). In mice, the lack of CD37 is paired with reduced T cell-dependent antibody-secreting cells and memory B cells, apparently due to the loss of CD37-mediated clustering of α 4 β 1 integrins (VLA-4) on germinal center B cells and decreased downstream activation of PI3K/AKT signaling and cell survival (5). Reflecting the expression pattern observed in normal lymphocytes, CD37 exhibits elevated expression in all mature B-cell lymphoid neoplasms, including most lymphoma subtypes, and absence in early progenitor cells or terminally differentiated plasma cells (6,8-14). In DLBCL, CD37 expression has been reported between 40% and 90% of cases across multiple studies performed using different antibodies (10,14-16). CD37-directed antibody- and, more recently, cellular-based approaches have shown preclinical (7,10-14,17-23) and early promising clinical activity (24-32). Among the CD37-targeting agents, naratuximab emtansine (Debio 1562, IMGN529) is an antibody-drug conjugate (ADC) that incorporates the anti-CD37 humanized IgG1 monoclonal antibody K7153A conjugated to the maytansinoid DM1, as payload, via the thioether linker, N-succinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC) (10). Based on the initial in vitro and in vivo evidence of anti-tumor activity in lymphoma and chronic lymphocytic leukemia (CLL) (7,10), naratuximab emtansine entered the clinical evaluation as a single agent. The phase 1 study exploring naratuximab emtansine enrolled 39 patients with relapsed/refractory B cell lymphoma (27). The overall response rate (ORR) was 13% across all patients and 22% in DLBCL patients, including the only observed complete remission (CR) (27). In preliminary results of a phase 2 trial exploring the combination of naratuximab emtansine with the anti-CD20 monoclonal antibody rituximab (18), based on positive preclinical data (18), the ORR was 45% in 76 patients with DLBCL with 24 CRs (32%), 57% in 14 patients with follicular lymphoma (five CR), 50% in four MCL patients (2 CR) (31). Here, we studied the pattern of activity of naratuximab emtansine across a large panel of cell lines derived from DLBCL and other lymphoma subtypes and characterized two resistance mechanisms to the ADC.
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6
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Magrin C, Bellafante M, Sola M, Piovesana E, Bolis M, Cascione L, Napoli S, Rinaldi A, Papin S, Paganetti P. Tau protein modulates an epigenetic mechanism of cellular senescence in human SH-SY5Y neuroblastoma cells. Front Cell Dev Biol 2023; 11:1232963. [PMID: 37842084 PMCID: PMC10569482 DOI: 10.3389/fcell.2023.1232963] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/21/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction: Progressive Tau deposition in neurofibrillary tangles and neuropil threads is the hallmark of tauopathies, a disorder group that includes Alzheimer's disease. Since Tau is a microtubule-associated protein, a prevalent concept to explain the pathogenesis of tauopathies is that abnormal Tau modification contributes to dissociation from microtubules, assembly into multimeric β-sheets, proteotoxicity, neuronal dysfunction and cell loss. Tau also localizes in the cell nucleus and evidence supports an emerging function of Tau in DNA stability and epigenetic modulation. Methods: To better characterize the possible role of Tau in regulation of chromatin compaction and subsequent gene expression, we performed a bioinformatics analysis of transcriptome data obtained from Tau-depleted human neuroblastoma cells. Results: Among the transcripts deregulated in a Tau-dependent manner, we found an enrichment of target genes for the polycomb repressive complex 2. We further describe decreased cellular amounts of the core components of the polycomb repressive complex 2 and lower histone 3 trimethylation in Tau deficient cells. Among the de-repressed polycomb repressive complex 2 target gene products, IGFBP3 protein was found to be linked to increased senescence induction in Tau-deficient cells. Discussion: Our findings propose a mechanism for Tau-dependent epigenetic modulation of cell senescence, a key event in pathologic aging.
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Affiliation(s)
- Claudia Magrin
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Cantonale Ospedaliero, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, PhD Program in Neurosciences, Università Della Svizzera Italiana, Lugano, Switzerland
| | - Martina Bellafante
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Cantonale Ospedaliero, Bellinzona, Switzerland
| | - Martina Sola
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Cantonale Ospedaliero, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, PhD Program in Neurosciences, Università Della Svizzera Italiana, Lugano, Switzerland
| | - Ester Piovesana
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Cantonale Ospedaliero, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, PhD Program in Neurosciences, Università Della Svizzera Italiana, Lugano, Switzerland
| | - Marco Bolis
- Functional Cancer Genomics Laboratory, Institute of Oncology Research, Università Della Svizzera Italiana, Bellinzona, Switzerland
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
- Lymphoma and Genomics Research Program, Institute of Oncology Research, Università Della Svizzera Italiana, Bellinzona, Switzerland
| | - Luciano Cascione
- Lymphoma and Genomics Research Program, Institute of Oncology Research, Università Della Svizzera Italiana, Bellinzona, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sara Napoli
- Lymphoma and Genomics Research Program, Institute of Oncology Research, Università Della Svizzera Italiana, Bellinzona, Switzerland
| | - Andrea Rinaldi
- Lymphoma and Genomics Research Program, Institute of Oncology Research, Università Della Svizzera Italiana, Bellinzona, Switzerland
| | - Stéphanie Papin
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Cantonale Ospedaliero, Bellinzona, Switzerland
| | - Paolo Paganetti
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Cantonale Ospedaliero, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, PhD Program in Neurosciences, Università Della Svizzera Italiana, Lugano, Switzerland
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7
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Chung EYL, Sartori G, Ponzoni M, Cascione L, Priebe V, Xu-Monette ZY, Fang X, Zhang M, Visco C, Tzankov A, Rinaldi A, Sgrignani J, Zucca E, Rossi D, Cavalli A, Inghirami G, Scott DW, Young KH, Bertoni F. ETS1 phosphorylation at threonine 38 is associated with the cell of origin of diffuse large B cell lymphoma and sustains the growth of tumour cells. Br J Haematol 2023; 203:244-254. [PMID: 37584198 DOI: 10.1111/bjh.19018] [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: 12/12/2022] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/17/2023]
Abstract
The transcriptional factor ETS1 is upregulated in 25% of diffuse large B cell lymphoma (DLBCL). Here, we studied the role of ETS1 phosphorylation at threonine 38, a marker for ETS1 activation, in DLBCL cellular models and clinical specimens. p-ETS1 was detected in activated B cell-like DLBCL (ABC), not in germinal centre B-cell-like DLBCL (GCB) cell lines and, accordingly, it was more common in ABC than GCB DLBCL diagnostic biopsies. MEK inhibition decreased both baseline and IgM stimulation-induced p-ETS1 levels. Genetic inhibition of phosphorylation of ETS1 at threonine 38 affected the growth and the BCR-mediated transcriptome program in DLBCL cell lines. Our data demonstrate that ETS1 phosphorylation at threonine 38 is important for the growth of DLBCL cells and its pharmacological inhibition could benefit lymphoma patients.
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Affiliation(s)
- Elaine Y L Chung
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Giulio Sartori
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Maurilio Ponzoni
- IRCCS San Raffaele Hospital Scientific Institute, Vita Salute San Raffaele University, Milan, Italy
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Valdemar Priebe
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | | | - Xiaosheng Fang
- Duke University Medical Center, Durham, North Carolina, USA
| | - Mingzhi Zhang
- Duke University Medical Center, Durham, North Carolina, USA
| | - Carlo Visco
- Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Alexandar Tzankov
- Pathology, Institute of Medical Genetics and Pathology, University Hospital, Basel, Switzerland
| | - Andrea Rinaldi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Jacopo Sgrignani
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, USI, Bellinzona, Switzerland
| | - Emanuele Zucca
- Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Davide Rossi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Andrea Cavalli
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, USI, Bellinzona, Switzerland
| | - Giorgio Inghirami
- Pathology and Laboratory Medicine Department, Weill Cornell Medicine, New York, New York, USA
| | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ken H Young
- Duke University Medical Center, Durham, North Carolina, USA
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
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8
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Canella A, Nieves HC, Sborov DW, Cascione L, Radomska HS, Smith E, Stiff A, Consiglio J, Caserta E, Rizzotto L, Zanesi N, Stefano V, Kaur B, Mo X, Byrd JC, Efebera YA, Hofmeister CC, Pichiorri F. Correction: HDAC inhibitor AR-42 decreases CD44 expression and sensitizes myeloma cells to lenalidomide. Oncotarget 2023; 14:837-838. [PMID: 37747363 PMCID: PMC10519243 DOI: 10.18632/oncotarget.28515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023] Open
Affiliation(s)
- Alessandro Canella
- Department of Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- These authors have contributed equally to this work
| | - Hector Cordero Nieves
- Department of Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- These authors have contributed equally to this work
| | - Douglas W. Sborov
- Department of Internal Medicine, Oncology/Hematology Fellowship, The Ohio State University, Columbus, OH, USA
| | - Luciano Cascione
- Lymphoma and Genomics Research Program, IOR Institute of Oncology Research, Bellinzona, Switzerland
| | - Hanna S. Radomska
- Department of Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Emily Smith
- Department of Internal Medicine, Biomedical Sciences Graduate Program, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Andrew Stiff
- Department of Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Jessica Consiglio
- Department of Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Present Address: Sanford Burnham Prebys Medical Discovery Insitute, La Jolla, CA, USA
| | - Enrico Caserta
- Department of Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Lara Rizzotto
- Department of Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Nicola Zanesi
- Department of Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Volinia Stefano
- Department of Internal Medicine, Biosystems Analysis, LTTA, Department of Morphology, Surgery and Experimental Medicine, Università degli Studi, Ferrara, Italy
| | - Balveen Kaur
- Department of Neurological Surgery, Dardinger Laboratory for Neuro-oncology and Neurosciences, The Ohio State University Medical Center, Columbus, Ohio, USA
| | - Xiaokui Mo
- Department of Biomedical Informatics, Center for Biostatistics, The Ohio State University, Columbus, OH, USA
| | - John C. Byrd
- Department of Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH, USA
| | - Yvonne A. Efebera
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH, USA
| | - Craig C. Hofmeister
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH, USA
| | - Flavia Pichiorri
- Department of Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, OH, USA
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9
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Spriano F, Aresu L, Cascione L, Risi G, Arribas AJ, Napoli S, Forster-Gross N, Bachmann F, Engelhardt M, Lane H, Bertoni F. The microtubule-targeted agent lisavanbulin (BAL101553) shows anti-tumor activity in lymphoma models. Am J Cancer Res 2023; 13:2076-2086. [PMID: 37293172 PMCID: PMC10244095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/16/2023] [Indexed: 06/10/2023] Open
Abstract
Microtubules are major components of the cellular cytoskeleton, ubiquitously founded in all eukaryotic cells. They are involved in mitosis, cell motility, intracellular protein and organelle transport, and maintenance of cytoskeletal shape. Avanbulin (BAL27862) is a microtubule-targeted agent (MTA) that promotes tumor cell death by destabilization of microtubules. Due to its unique binding to the colchicine site of tubulin, differently from other MTAs, avanbulin has previously shown activity in solid tumor cell lines. Its prodrug, lisavanbulin (BAL101553), has shown early signs of clinical activity, especially in tumors with high EB1 expression. Here, we assessed the preclinical anti-tumor activity of avanbulin in diffuse large B cell lymphoma (DLBCL) and the pattern of expression of EB1 in DLBCL cell lines and clinical specimens. Avanbulin showed a potent in vitro anti-lymphoma activity, which was mainly cytotoxic with potent and rapid apoptosis induction. Median IC50 was around 10 nM in both ABC and GCB-DLBCL. Half of the cell lines tested showed an induction of apoptosis already in the first 24 h of treatment, the other half in the first 48 h. EB1 showed expression in DLBCL clinical specimens, opening the possibility for a cohort of patients that could potentially benefit from treatment with lisavanbulin. These data show the basis for further preclinical and clinical evaluation of lisavanbulin in the lymphoma field.
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Affiliation(s)
- Filippo Spriano
- Institute of Oncology Research, Faculty of Biomedical Sciences, USIBellinzona, Switzerland
| | - Luca Aresu
- Department of Veterinary Science, University of TurinGrugliasco, Turin, Italy
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USIBellinzona, Switzerland
- SIB Swiss Institute of BioinformaticsLausanne, Switzerland
| | - Giorgia Risi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USIBellinzona, Switzerland
| | - Alberto J Arribas
- Institute of Oncology Research, Faculty of Biomedical Sciences, USIBellinzona, Switzerland
- SIB Swiss Institute of BioinformaticsLausanne, Switzerland
| | - Sara Napoli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USIBellinzona, Switzerland
| | | | - Felix Bachmann
- Basilea Pharmaceutica International LtdAllschwill, Switzerland
| | - Marc Engelhardt
- Basilea Pharmaceutica International LtdAllschwill, Switzerland
| | - Heidi Lane
- Basilea Pharmaceutica International LtdAllschwill, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USIBellinzona, Switzerland
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero CantonaleBellinzona, Switzerland
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10
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Robin P, Barnabei L, Marocco S, Pagnoncelli J, Nicolis D, Tarantelli C, Tavilla AC, Robortella R, Cascione L, Mayoraz L, Journot CMA, Mensi M, Bertoni F, Stefanini I, Gerber-Lemaire S. A DNA biosensors-based microfluidic platform for attomolar real-time detection of unamplified SARS-CoV-2 virus. Biosens Bioelectron X 2023; 13:100302. [PMID: 36589921 PMCID: PMC9793959 DOI: 10.1016/j.biosx.2022.100302] [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] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/29/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
The emergence of the coronavirus 2019 (COVID-19) arose the need for rapid, accurate and massive virus detection methods to control the spread of infectious diseases. In this work, a device, deployable in non-medical environments, has been developed for the detection of non-amplified SARS-CoV-2 RNA. A SARS-CoV-2 specific probe was designed and covalently immobilized at the surface of glass slides to fabricate a DNA biosensor. The resulting system was integrated in a microfluidic platform, in which viral RNA was extracted from non-treated human saliva, before hybridizing at the surface of the sensor. The formed DNA/RNA duplex was detected in presence of SYBR Green I using an opto-electronic system, based on a high-power LED and a photo multiplier tube, which convert the emitted fluorescence into an electrical signal that can be processed in less than 10 min. The limit of detection of the resulting microfluidic platform reached six copies of viral RNA per microliter of sample (equal to 10 aM) and satisfied the safety margin. The absence of non-specific adsorption and the selectivity for SARS-CoV-2 RNA were established. In addition, the designed device could be applicable for the detection of a variety of viruses by simple modification of the immobilized probe.
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Affiliation(s)
- Perrine Robin
- Group for Functionalized Biomaterials, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Laura Barnabei
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Via Francesco Chiesa 5, CH-6500, Bellinzona, Switzerland
| | - Stefano Marocco
- Medical Devices area, Institute of Digital Technologies for Personalized Healthcare - MeDiTech, Department of Innovative Technologies, University of Applied Sciences of Southern Switzerland, Via la Santa 1, CH-6962, Lugano, Viganello, Switzerland
| | - Jacopo Pagnoncelli
- Medical Devices area, Institute of Digital Technologies for Personalized Healthcare - MeDiTech, Department of Innovative Technologies, University of Applied Sciences of Southern Switzerland, Via la Santa 1, CH-6962, Lugano, Viganello, Switzerland
| | - Daniele Nicolis
- Department of Innovative Technologies, University of Applied Sciences of Southern Switzerland, Via la Santa 1, CH-6962, Lugano, Viganello, Switzerland
| | - Chiara Tarantelli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Via Francesco Chiesa 5, CH-6500, Bellinzona, Switzerland
| | - Agatino Christian Tavilla
- Department of Innovative Technologies, University of Applied Sciences of Southern Switzerland, Via la Santa 1, CH-6962, Lugano, Viganello, Switzerland
| | - Roberto Robortella
- Department of Innovative Technologies, University of Applied Sciences of Southern Switzerland, Via la Santa 1, CH-6962, Lugano, Viganello, Switzerland
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Via Francesco Chiesa 5, CH-6500, Bellinzona, Switzerland
| | - Lucas Mayoraz
- Group for Functionalized Biomaterials, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Céline M A Journot
- Group for Functionalized Biomaterials, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Mounir Mensi
- ISIC-XRDSAP, EPFL Valais-Wallis, Rue de l'Industrie 17, CH-1951, Sion, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Via Francesco Chiesa 5, CH-6500, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, CH-6500, Bellinzona, Switzerland
| | - Igor Stefanini
- Medical Devices area, Institute of Digital Technologies for Personalized Healthcare - MeDiTech, Department of Innovative Technologies, University of Applied Sciences of Southern Switzerland, Via la Santa 1, CH-6962, Lugano, Viganello, Switzerland
- Department of Innovative Technologies, University of Applied Sciences of Southern Switzerland, Via la Santa 1, CH-6962, Lugano, Viganello, Switzerland
| | - Sandrine Gerber-Lemaire
- Group for Functionalized Biomaterials, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
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11
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Arribas AJ, Napoli S, Cascione L, Barnabei L, Sartori G, Cannas E, Gaudio E, Tarantelli C, Mensah AA, Spriano F, Zucchetto A, Rossi FM, Rinaldi A, de Moura MC, Stathis A, Stussi G, Gattei V, Brown JR, Esteller M, Zucca E, Rossi D, Bertoni F. Abstract 394: ERBB4-mediated signaling is a mediator of resistance to BTK and PI3K inhibitors in B cell lymphoid neoplasms. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-394] [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: Marginal zone lymphoma (MZL) is an indolent yet incurable B cell malignancy. Two BTK inhibitors, ibrutinib and zanubrutinib, are FDA approved for relapsed/refractory MZL patients. PI3K inhibitors have also shown clinical activity. The identification of the mechanisms of resistance can provide useful information to optimize the use of the agents. We previously reported an IL6 driven MZL model of PI3K inhibitors resistance developed by prolonged exposure to the PI3Kδ inhibitor idelalisib (Arribas, Haematologica 2022). Here, we present the detailed characterization of a second model with resistance to both BTK and PI3K inhibitors.
Methods: MTT assay. RNA-Seq, whole exome sequencing, miRNA and methylation profiling. FACS and ELISA analyses.
Results: Resistant cells, developed by continuous exposure of the cell line Karpas1718 to idelalisib, showed resistance to various inhibitors of BTK (ibrutinib, zanubrutinib, acalabrutinib and pirtobrutinib) and PI3K (idelalisib, duvelisib, copanlisib and umbralisib). No mutations affecting BTK, PLCG2 or CXCR4 were identified in resistant cells, which had higher expression of genes involved in ERBB signaling (HBEGF, NRG2, ERBB4), cell proliferation (PBK, MKI67, TCL1A) and DNA recombination (RAG1, RAG2) than parental cells. We confirmed cell surface ERBB4 up-regulation, and the cytoplasmatic expression and secretion of its ligand HBEGF in resistant cells, which led to increased levels of p-AKT and p-ERK. The miRNAs miR-29c and let-7c, known negative regulators of the HBEGF-ERBB axis, were fully methylated and down-regulated in resistant compared to parental cells. ERBB4 genetic silencing improved sensitivity to PI3Kδ inhibitor, and exposure to let-7c or miR-29c mimics decreased secreted HBEGF and recovered sensitivity to PI3K inhibitors in resistant cells. Addition of recombinant HBEGF (rHBEGF) induced resistance to BTK and to PI3K inhibitors in parental cells and in other lymphoma models including mantle cell lymphomas and diffuse large B cell lymphomas (DLBCL). The rHBEGF induced resistance was reverted adding the ERBB inhibitor lapatinib. To extend our findings to the clinical context, using two MZL and one DLBCL expression datasets, we showed HBEGF and ERBB4 expression in clinical specimens. Finally, HBEGF levels appeared elevated in the serum of CLL patients with primary or acquired resistance to PI3Kδ or to BTK inhibitors, compared to patients responding to the drugs and paired for similar clinical features.
Conclusions: We characterized a novel B cell lymphoma model of secondary resistance to BTK and PI3K inhibitors. Our results indicate that epigenetic plasticity led to the activation of HBEGF-ERBB signaling sustaining resistance to BTK/PI3K inhibitors, which can be overcome using epigenetic agents and ERBB inhibitors. These therapeutics approaches could be tested in novel clinical trials. AJA, SN: equally contributed.
Citation Format: Alberto J. Arribas, Sara Napoli, Luciano Cascione, Laura Barnabei, Giulio Sartori, Eleonora Cannas, Eugenio Gaudio, Chiara Tarantelli, Afua A. Mensah, Filippo Spriano, Antonella Zucchetto, Francesca M. Rossi, Andrea Rinaldi, Manuel Castro de Moura, Anastasios Stathis, Georg Stussi, Valter Gattei, Jennifer R. Brown, Manel Esteller, Emanuele Zucca, Davide Rossi, Francesco Bertoni. ERBB4-mediated signaling is a mediator of resistance to BTK and PI3K inhibitors in B cell lymphoid neoplasms [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 394.
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Affiliation(s)
| | - Sara Napoli
- 1Institute of Oncology Research, Bellinzona, Switzerland
| | | | - Laura Barnabei
- 1Institute of Oncology Research, Bellinzona, Switzerland
| | - Giulio Sartori
- 1Institute of Oncology Research, Bellinzona, Switzerland
| | | | - Eugenio Gaudio
- 1Institute of Oncology Research, Bellinzona, Switzerland
| | | | - Afua A. Mensah
- 1Institute of Oncology Research, Bellinzona, Switzerland
| | | | | | | | - Andrea Rinaldi
- 1Institute of Oncology Research, Bellinzona, Switzerland
| | | | | | - Georg Stussi
- 4Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Valter Gattei
- 2Centro di Riferimento Oncologico di Aviano – CRO, Aviano, Italy
| | - Jennifer R. Brown
- 5Chronic Lymphocytic Leukemia Center, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | - Manel Esteller
- 3Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Emanuele Zucca
- 1Institute of Oncology Research, Bellinzona, Switzerland
| | - Davide Rossi
- 1Institute of Oncology Research, Bellinzona, Switzerland
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12
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Johnson Z, Tarantelli C, Civanelli E, Cascione L, Spriano F, Fraser A, Shah P, Nomanbhoy T, Napoli S, Rinaldi A, Niewola-Staszkowska K, Lahn M, Perrin D, Wenes M, Migliorini D, Bertoni F, van der Veen L, Di Conza G. IOA-244 is a Non-ATP-competitive, Highly Selective, Tolerable PI3K Delta Inhibitor That Targets Solid Tumors and Breaks Immune Tolerance. Cancer Res Commun 2023; 3:576-591. [PMID: 37066023 PMCID: PMC10103717 DOI: 10.1158/2767-9764.crc-22-0477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/21/2022] [Accepted: 03/14/2023] [Indexed: 04/18/2023]
Abstract
PI3K delta (PI3Kδ) inhibitors are used to treat lymphomas but safety concerns and limited target selectivity curbed their clinical usefulness. PI3Kδ inhibition in solid tumors has recently emerged as a potential novel anticancer therapy through the modulation of T-cell responses and direct antitumor activity. Here we report the exploration of IOA-244/MSC2360844, a first-in-class non-ATP-competitive PI3Kδ inhibitor, for the treatment of solid tumors. We confirm IOA-244's selectivity as tested against a large set of kinases, enzymes, and receptors. IOA-244 inhibits the in vitro growth of lymphoma cells and its activity correlates with the expression levels of PIK3CD, suggesting cancer cell-intrinsic effects of IOA-244. Importantly, IOA-244 inhibits regulatory T cell proliferation while having limited antiproliferative effects on conventional CD4+ T cells and no effect on CD8+ T cells. Instead, treatment of CD8 T cells with IOA-244 during activation, favors the differentiation of memory-like, long-lived CD8, known to have increased antitumor capacity. These data highlight immune-modulatory properties that can be exploited in solid tumors. In CT26 colorectal and Lewis lung carcinoma lung cancer models, IOA-244 sensitized the tumors to anti-PD-1 (programmed cell death protein 1) treatment, with similar activity in the Pan-02 pancreatic and A20 lymphoma syngeneic mouse models. IOA-244 reshaped the balance of tumor-infiltrating cells, favoring infiltration of CD8 and natural killer cells, while decreasing suppressive immune cells. IOA-244 presented no detectable safety concerns in animal studies and is currently in clinical phase Ib/II investigation in solid and hematologic tumors. Significance IOA-244 is a first-in-class non-ATP-competitive, PI3Kδ inhibitor with direct antitumor in vitro activity correlated with PI3Kδ expression. The ability to modulate T cells, in vivo antitumor activity in various models with limited toxicity in animal studies provides the rationale for the ongoing trials in patients with solid tumors and hematologic cancers.
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Affiliation(s)
| | - Chiara Tarantelli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Elisa Civanelli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- SIB, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Filippo Spriano
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Amy Fraser
- Cancer Research Horizons, Jonas Webb Building, Cambridge, United Kingdom
| | - Pritom Shah
- Cancer Research Horizons, Jonas Webb Building, Cambridge, United Kingdom
| | | | - Sara Napoli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Andrea Rinaldi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | | | | | | | - Mathias Wenes
- Brain Tumor and Immune Cell Engineering Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Center for Translational Research in Onco-Hematology, University of Geneva, Geneva, Switzerland
- Swiss Cancer Center Leman, Geneva and Lausanne, Switzerland
| | - Denis Migliorini
- Brain Tumor and Immune Cell Engineering Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Center for Translational Research in Onco-Hematology, University of Geneva, Geneva, Switzerland
- Swiss Cancer Center Leman, Geneva and Lausanne, Switzerland
- Department of Oncology, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Corresponding Authors: Giusy Di Conza, iOnctura SA, Geneva 1202, Switzerland. Phone: 417-6427-1182; E-mail: ; Lars van der Veen, ; and Francesco Bertoni,
| | - Lars van der Veen
- iOnctura SA, Geneva, Switzerland
- Corresponding Authors: Giusy Di Conza, iOnctura SA, Geneva 1202, Switzerland. Phone: 417-6427-1182; E-mail: ; Lars van der Veen, ; and Francesco Bertoni,
| | - Giusy Di Conza
- iOnctura SA, Geneva, Switzerland
- Corresponding Authors: Giusy Di Conza, iOnctura SA, Geneva 1202, Switzerland. Phone: 417-6427-1182; E-mail: ; Lars van der Veen, ; and Francesco Bertoni,
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13
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Spriano F, Tarantelli C, Arribas AJ, Gaudio E, Cascione L, Aresu L, Rinaldi A, Zucca E, Rossi D, Stathis A, Murone M, Radtke F, Lehal R, Bertoni F. In vitro anti-lymphoma activity of the first-in-class pan-NOTCH transcription inhibitor CB-103. Br J Haematol 2023; 200:669-672. [PMID: 36484636 DOI: 10.1111/bjh.18576] [Citation(s) in RCA: 1] [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: 08/25/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022]
Affiliation(s)
- Filippo Spriano
- Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, Switzerland
| | - Chiara Tarantelli
- Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, Switzerland
| | - Alberto J Arribas
- Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Eugenio Gaudio
- Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, Switzerland
| | - Luciano Cascione
- Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Luca Aresu
- Department of Veterinary Science, University of Turin, Grugliasco, Turin, Italy
| | - Andrea Rinaldi
- Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, Switzerland
| | - Emanuele Zucca
- Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, Switzerland.,Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Davide Rossi
- Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, Switzerland.,Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Anastasios Stathis
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Sciences, USI, Lugano, Switzerland
| | | | - Freddy Radtke
- Swiss Institute for Experimental Cancer Research, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Francesco Bertoni
- Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, Switzerland.,Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
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14
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Bertoni F, Tarantelli C, Spriano F, Cascione L, Civanelli E, Cannas E, Mensah A, Arribas A, Napoli S, Rinaldi A, Stathis A, Niewola K, Di Conza G, Lahn M, Santoro A, Carlo-Stella C. 53P Characterization of the non-ATP competitive PI3Kdelta inhibitor IOA-244 in lymphoma models: From single agent to combination screen and clinical investigation. ESMO Open 2023. [DOI: 10.1016/j.esmoop.2023.100911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
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15
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Arribas AJ, Napoli S, Cascione L, Barnabei L, Sartori G, Cannas E, Gaudio E, Tarantelli C, Mensah AA, Spriano F, Zucchetto A, Rossi FM, Rinaldi A, de Moura MC, Jovic S, Pittau RB, Stathis A, Stussi G, Gattei V, Brown JR, Esteller M, Zucca E, Rossi D, Bertoni F. ERBB4-mediated signaling is a mediator of resistance to BTK and PI3K inhibitors in B cell lymphoid neoplasms. bioRxiv 2023:2023.01.01.522017. [PMID: 36711490 PMCID: PMC9881865 DOI: 10.1101/2023.01.01.522017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BTK and PI3K inhibitors are among the drugs approved for the treatment of patients with lymphoid neoplasms. Although active, their ability to lead as single agents to long-lasting complete remission is rather limited especially in the lymphoma setting. This indicates that tumor cells often develop resistance to the drugs. Here, we show that the overexpression of ERBB4 and its ligands represents a modality for B cell neoplastic cells to bypass the anti-tumor activity of BTK and PI3K inhibitors and that targeted pharmacological interventions can restore sensitivity to the small molecules. We started from a marginal zone lymphoma (MZL) cell line, Karpas-1718, kept under prolonged exposure to the PI3Kδ inhibitor idelalisib until acquisition of resistance, or with no drug. Cells underwent transcriptome, miRNA and methylation profiling, whole exome sequencing, and pharmacological screening which led to the identification of the overexpression of ERBB4 and its ligands HBEGF and NRG2 in the resistant cells. Cellular and genetic experiments demonstrated the involvement of this axis in blocking the anti-tumor activity of various BTK and PI3K inhibitors, currently used in the clinical setting. Addition of recombinant HBEGF induced resistance to BTK and PI3K inhibitors in parental cells but also in additional lymphoma models. Combination with the ERBB inhibitor lapatinib was beneficial in resistant cells and in other lymphoma models already expressing the identified resistance factors. Multi-omics analysis underlined that an epigenetic reprogramming affected the expression of the resistance-related factors, and pretreatment with demethylating agents or EZH2 inhibitors overcame the resistance. Resistance factors were shown to be expressed in clinical samples, further extending the findings of the study. In conclusions, we identified a novel ERBB4-driven mechanism of resistance to BTK and PI3K inhibitors and treatments that appear to overcome it. Key points A mechanism of secondary resistance to the PI3Kδ and BTK inhibitors in B cell neoplasms driven by secreted factors.Resistance can be reverted by targeting ERBB signaling.
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16
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Virgilio T, Bordini J, Cascione L, Sartori G, Latino I, Molina Romero D, Leoni C, Akhmedov M, Rinaldi A, Arribas AJ, Morone D, Seyed Jafari SM, Bersudsky M, Ottolenghi A, Kwee I, Chiaravalli AM, Sessa F, Hunger RE, Bruno A, Mortara L, Voronov E, Monticelli S, Apte RN, Bertoni F, Gonzalez SF. Subcapsular Sinus Macrophages Promote Melanoma Metastasis to the Sentinel Lymph Nodes via an IL1α-STAT3 Axis. Cancer Immunol Res 2022; 10:1525-1541. [PMID: 36206577 PMCID: PMC9716256 DOI: 10.1158/2326-6066.cir-22-0225] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/18/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022]
Abstract
During melanoma metastasis, tumor cells originating in the skin migrate via lymphatic vessels to the sentinel lymph node (sLN). This process facilitates tumor cell spread across the body. Here, we characterized the innate inflammatory response to melanoma in the metastatic microenvironment of the sLN. We found that macrophages located in the subcapsular sinus (SS) produced protumoral IL1α after recognition of tumoral antigens. Moreover, we confirmed that the elimination of LN macrophages or the administration of an IL1α-specific blocking antibody reduced metastatic spread. To understand the mechanism of action of IL1α in the context of the sLN microenvironment, we applied single-cell RNA sequencing to microdissected metastases obtained from animals treated with the IL1α-specific blocking antibody. Among the different pathways affected, we identified STAT3 as one of the main targets of IL1α signaling in metastatic tumor cells. Moreover, we found that the antitumoral effect of the anti-IL1α was not mediated by lymphocytes because Il1r1 knockout mice did not show significant differences in metastasis growth. Finally, we found a synergistic antimetastatic effect of the combination of IL1α blockade and STAT3 inhibition with stattic, highlighting a new immunotherapy approach to preventing melanoma metastasis.
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Affiliation(s)
- Tommaso Virgilio
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Joy Bordini
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland.,GenomSys SA, Lugano, Switzerland
| | - Luciano Cascione
- Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Giulio Sartori
- Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Irene Latino
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Daniel Molina Romero
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland.,Graduate School Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Cristina Leoni
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Murodzhon Akhmedov
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland.,BigOmics Analytics, Lugano, Switzerland
| | - Andrea Rinaldi
- Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Alberto J. Arribas
- Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Diego Morone
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - S. Morteza Seyed Jafari
- Department of Dermatology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Marina Bersudsky
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Aner Ottolenghi
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ivo Kwee
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland.,BigOmics Analytics, Lugano, Switzerland
| | - Anna Maria Chiaravalli
- Unit of Pathology, ASST dei Sette Laghi, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Fausto Sessa
- Unit of Pathology, ASST dei Sette Laghi, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Robert E. Hunger
- Department of Dermatology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Antonino Bruno
- Laboratory of Innate Immunity, Unit of Molecular Pathology, Biochemistry, and Immunology, IRCCS MultiMedica, Milan, Italy.,Laboratory of Immunology and General Pathology, Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Lorenzo Mortara
- Laboratory of Immunology and General Pathology, Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Elena Voronov
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Silvia Monticelli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Ron N. Apte
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Francesco Bertoni
- Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland.,Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland
| | - Santiago F. Gonzalez
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland.,Corresponding Author: Santiago F. Gonzalez, Institute for Research in Biomedicine, via Francesco Chiesa 5. CH-6500 Bellinzona. Switzerland. Phone: +41 58 666 7226; E-mail:
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Alderuccio JP, Reis IM, Habermann TM, Link BK, Thieblemont C, Conconi A, Larson MC, Cascione L, Zhao W, Cerhan JR, Zucca E, Lossos IS. Revised MALT-IPI: A new predictive model that identifies high-risk patients with extranodal marginal zone lymphoma. Am J Hematol 2022; 97:1529-1537. [PMID: 36057138 PMCID: PMC9847507 DOI: 10.1002/ajh.26715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/11/2022] [Accepted: 08/29/2022] [Indexed: 01/31/2023]
Abstract
Extranodal marginal zone lymphoma (EMZL) is a heterogeneous disease with a subset of patients exhibiting a more aggressive course. We previously reported that EMZL with multiple mucosal sites (MMS) at diagnosis is characterized by shorter survival. To better recognize patients with different patterns of progression-free survival (PFS) we developed and validated a new prognostic index primarily based on patient's disease characteristics. We derived the "Revised mucosa-associated lymphoid tissue International Prognostic Index" (Revised MALT-IPI) in a large data set (n = 397) by identifying candidate variables that showed highest prognostic association with PFS. The revised MALT-IPI was validated in two independent cohorts, from the University of Iowa/Mayo Clinic (n = 297) and from IELSG-19 study (n = 400). A stepwise Cox regression analysis yielded a model including four independent predictors of shorter PFS. Revised MALT-IPI has scores ranging from 0 to 5, calculated as a sum of one point for each of the following- age >60 years, elevated LDH, and stage III-IV; and two points for MMS. In the training cohort, the Revised MALT-IPI defined four risk groups: low risk (score 0, reference group), low-medium risk (score 1, HR = 1.85, p = .008), medium-high risk (score 2, HR = 3.84, p < .0001), and high risk (score 3+, HR = 8.48, p < .0001). Performance of the Revised MALT-IPI was similar in external validation cohorts. Revised MALT-IPI is a new index centered on disease characteristics that provides robust risk-stratification identifying a group of patients characterized by earlier progression of disease. Revised MALT-IPI can allow a more disease-adjusted management of patients with EMZL in clinical trials and practice.
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Affiliation(s)
| | - Isildinha M. Reis
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
- Biostatistics and Bioinformatics Shared Resource, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | | | - Brian K. Link
- Division of Hematology, Oncology and Bone and Marrow Transplantation, University of Iowa, Iowa City, IA, USA
| | - Catherine Thieblemont
- APHP, Hôpital Saint-Louis, Service d’hémato-oncologie, DMU DHI, Université de Paris, Paris, France
| | | | - Melissa C. Larson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Luciano Cascione
- Clinic of Medical Oncology, Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Wei Zhao
- Biostatistics and Bioinformatics Shared Resource, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - James R. Cerhan
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Emanuele Zucca
- Clinic of Medical Oncology, Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Institute of Oncology Research, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, Switzerland
- Department of Medical Oncology, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Izidore S. Lossos
- Division of Hematology, Sylvester Comprehensive Cancer Center, Miami, FL, USA
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Garofalo M, Romano G, Di Leva G, Nuovo G, Jeon YJ, Ngankeu A, Sun J, Lovat F, Alder H, Condorelli G, Engelman JA, Ono M, Rho JK, Cascione L, Volinia S, Nephew KP, Croce CM. Retraction Note: EGFR and MET receptor tyrosine kinase-altered microRNA expression induces tumorigenesis and gefitinib resistance in lung cancers. Nat Med 2022; 28:2436. [PMID: 36195688 PMCID: PMC9675728 DOI: 10.1038/s41591-022-02044-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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19
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Tarantelli C, Spriano F, Cascione L, Civanelli E, Cannas E, Mensah A, Arribas A, Rinaldi A, Stathis A, Di Conza G, Niewola-Staszkowska K, Lahn M, Bertoni F. Non-ATP competitive inhibition of PI3Kδ with IOA-244 shows anti-lymphoma activity. Eur J Cancer 2022. [DOI: 10.1016/s0959-8049(22)01012-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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20
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Sartori G, Priebe V, Cascione L, Chung EY, Favre-Juilland M, Napoli S, Arribas A, Rinaldi A, Miazza MT, Bertoni F. Abstract A14: The RNA helicase DDX21 cooperates with ETS1 and FLI1 in cell cycle and RNA processing. Blood Cancer Discov 2022. [DOI: 10.1158/2643-3249.lymphoma22-a14] [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] Open
Abstract
Abstract
Introduction. The two ETS transcription factors ETS1 and FLI1 are co-mapped in the 11q24.3 region recurrently gained in up to 25% of diffuse large B cell lymphomas (DLBCL) (Bonetti et al, 2013). The two proteins largely co-regulate a series of genes involved in B-cell signaling, differentiation and cell cycle (Priebe et al, 2020; Sartori et al, 2021). While FLI1 is expressed at a higher level in DLBCL of the germinal center B-cell (GCB) type than in the activated B-cell-like (ABC) DLBCL, ETS1 is more expressed in the latter subgroup. We and others have reported preclinical anti-tumor activity in lymphomas and other tumors with small molecules blocking the binding of ETS factors and RNA helicases (Erkizan et al, 2009; Spriano et al, 2019), and encouraging clinical data are coming from the first trials enrolling Ewing Sarcoma patients (Ludwig et al, 2020). Here, proteomic experiments were performed to investigate ETS1 interactome in DLBCL. Methods. To investigate interaction partners, protein precipitation was performed using streptavidin beads to pull down strep-tagged ETS1 in DLBCL ABC cell line, HBL-1, followed by Liquid Chromatography tandem Mass Spectrometry (LC-MS/MS). Shotgun proteomics analysis identified biologically relevant ETS1 protein interactors, with a spectral count above four, that were validated by normal and reverse co-immunoprecipitation experiments. Transcriptome analysis was done via RNASeq after DDX21 siRNAs silencing in four DLBCL cell lines, two derived from ABC (HBL1 and U2932) and two from GCB (OCI-Ly1 and VAL). Results. Identified ETS1 interactors in the ABC DLBCL HBL-1 included proteins related to RNA processing, more specifically in spliceosome (NOP56 and ALYREF) and in ribosome biogenesis (SF3B1 and DDX21). Among these, we focused on the novel interactor DDX21, an RNA helicase also regulated by FLI1 (Sartori et al, 2021). DDX21 was found differentially expressed between GCB and ABC DLBCL, with higher expression in the latter (P<0.001) (GSE98588: n= 117 cases, phs001444.v2.p1: n= 432 cases, GSE95013: n= 33 cases, and GSE10846, n= 350 cases). When we silenced DDX21 with siRNAs, toxicity was seen in both ABC and GCB cell lines. To better characterize the role of DDX21 as a transcriptional factor in DLBCL and to further investigate its link with ETS1 and FLI1 we obtained RNASeq transcriptome after DDX21 silencing. Transcriptional profiling and functional annotation of transcripts regulated by DDX21 identified genes coding proteins involved in cell cycle (FDR <0.001), ribosomes (FDR <0.001) and spliceosome (FDR <0.001).Conclusions. ETS1 interacts with proteins involved in spliceosome and in ribosome biogenesis, including DDX21. More expressed in ABC than GCB DLBCL, DDX21 appears essential for the survival of lymphoma cells by regulating cell cycle and RNA processing. The interaction between ETS1 and DDX21 offers an additional therapeutic opportunity against DLBCL cells.
Citation Format: Giulio Sartori, Valdemar Priebe, Luciano Cascione, Elaine Y.L. Chung, Mélanie Favre-Juilland, Sara Napoli, Alberto Arribas, Andrea Rinaldi, Margot Thome Miazza, Francesco Bertoni. The RNA helicase DDX21 cooperates with ETS1 and FLI1 in cell cycle and RNA processing [abstract]. In: Proceedings of the Third AACR International Meeting: Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2022 Jun 23-26; Boston, MA. Philadelphia (PA): AACR; Blood Cancer Discov 2022;3(5_Suppl):Abstract nr A14.
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Affiliation(s)
- Giulio Sartori
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,
| | - Valdemar Priebe
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,
| | - Luciano Cascione
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,
| | - Elaine Y.L. Chung
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,
| | | | - Sara Napoli
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,
| | - Alberto Arribas
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,
| | - Andrea Rinaldi
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,
| | | | - Francesco Bertoni
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,
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Sartori G, Cascione L, Matkovic M, Matsunami H, Cavalli A, Bertoni F. Abstract A05: Olfactory receptors as a new therapeutic target in lymphomas. Blood Cancer Discov 2022. [DOI: 10.1158/2643-3249.lymphoma22-a05] [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] Open
Abstract
Abstract
Background. Diffuse large B cell lymphoma (DLBCL) and mantle cell lymphoma (MCL) are aggressive lymphomas in which up to 40% of patients are still in need of therapy. G protein-coupled receptors (GPCRs) are integral membrane proteins that mediate cellular responses to endogenous and exogenous stimuli and are implicated in the pathophysiology of various diseases: CXCR3/4/5, S1PR1/2/3, or GPR34 are GPCRs already studied in lymphomas. The olfactory receptors (ORs) are also GPCRs, initially identified and characterized for their expression in olfactory cells but now shown to be expressed in various tissues. OR51E1 is known as prostate-specific G protein-coupled receptor 2 (PSGR2) due to its expression in prostate cancer, OR2B6 and OR2W3 are expressed in breast cancer, and OR51E1 in melanoma. Here, we studied OR13A1 in lymphoma cell lines and clinical specimens. Methods. RNA-Seq and real-time PCR for evaluating the expression of ORs in lymphoma cell lines. Gene expression data for clinical samples were obtained from public datasets. OR13A1 silencing was performed with both siRNAs (OCI-Ly1 and U2932) and doxycycline-inducible shRNAs (U2932 and VAL); viability was assessed after 3 days using MTT and even longer with live imaging. Computer modelling was performed using available ligands for the murine orthologue Olfr211. Results. Various ORs were expressed across a large panel of B cell lymphoma cell lines. In particular, OR13A1 was expressed in 35/47 cell lines and, mostly, derived from DLBCL and MCL. Among DLBCL, the expression was higher in cell lines derived from the germinal center (GC) B-cell type (GCB) rather than from activated B cell like (ABC) DLBCL (P value = 0.03). A similar pattern was observed in DLBCL patients: higher expression in GCB than ABC and in EZB than MCD (P < 0.001). OR13A1 also appeared higher in normal GC cells than in naïve and memory B cells. OR13A1 expression appears to identify GCB DLBCL (P value = 0.009) and MCL (P value = 0.006) patients with inferior outcome. Silencing of OR13A1 with siRNAs in GCB and ABC DLBCL cells (OCI-Ly1 and U2932) caused > 50% reduction in cell viability, and downregulation of pERK levels. Viability data were confirmed using a doxycycline-inducible shRNA system and an Incucyte live cell imaging instrument. Natural compounds reported as ligands for the murine orthologue Olfr211 or in silico identified to bind as agonists (ex: tyramine) increased cell line growth and compounds predicted to bind as antagonists (ex: cyclohexanone) decreased the cell viability in the presence but not in the absence of the GPCR. Conclusion. OR13A1 gene appeared more abundantly expressed in lymphomas compared to others ORs, in particular it was more expressed in MCL and in GCB DLBCL with a possible impact on clinical outcome. Genetic and chemical experiments showed that this GPCR has an essential function in lymphoma cells and represents a novel therapeutic target.
Citation Format: Giulio Sartori, Luciano Cascione, Milos Matkovic, Hiro Matsunami, Andrea Cavalli, Francesco Bertoni. Olfactory receptors as a new therapeutic target in lymphomas [abstract]. In: Proceedings of the Third AACR International Meeting: Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2022 Jun 23-26; Boston, MA. Philadelphia (PA): AACR; Blood Cancer Discov 2022;3(5_Suppl):Abstract nr A05.
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Affiliation(s)
- Giulio Sartori
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,
| | - Luciano Cascione
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,
| | - Milos Matkovic
- 2Institute for Research in Biomedicine, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,
| | | | - Andrea Cavalli
- 2Institute for Research in Biomedicine, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,
| | - Francesco Bertoni
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,
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Casadei L, Sarchet P, de Faria FCC, Calore F, Nigita G, Tahara S, Cascione L, Wabitsch M, Hornicek FJ, Grignol V, Croce CM, Pollock RE. In situ hybridization to detect DNA amplification in extracellular vesicles. J Extracell Vesicles 2022; 11:e12251. [PMID: 36043432 PMCID: PMC9428764 DOI: 10.1002/jev2.12251] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 07/20/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 11/07/2022] Open
Abstract
EVs have emerged as an important component in tumour initiation, progression and metastasis. Although notable progresses have been made, the detection of EV cargoes remain significantly challenging for researchers to practically use; faster and more convenient methods are required to validate the EV cargoes, especially as biomarkers. Here we show, the possibility of examining embedded EVs as substrates to be used for detecting DNA amplification through ultrasensitive in situ hybridization (ISH). This methodology allows the visualization of DNA targets in a more direct manner, without time consuming optimization steps or particular expertise. Additionally, formalin‐fixed paraffin‐embedded (FFPE) blocks of EVs allows long‐term preservation of samples, permitting future studies. We report here: (i) the successful isolation of EVs from liposarcoma tissues; (ii) the EV embedding in FFPE blocks (iii) the successful selective, specific ultrasensitive ISH examination of EVs derived from tissues, cell line, and sera; (iv) and the detection of MDM2 DNA amplification in EVs from liposarcoma tissues, cell lines and sera. Ultrasensitive ISH on EVs would enable cargo study while the application of ISH to serum EVs, could represent a possible novel methodology for diagnostic confirmation. Modification of probes may enable researchers to detect targets and specific DNA alterations directly in tumour EVs, thereby facilitating detection, diagnosis, and improved understanding of tumour biology relevant to many cancer types.
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Affiliation(s)
- Lucia Casadei
- The Ohio State University Comprehensive Cancer CenterColumbusOhioUSA
| | - Patricia Sarchet
- The Ohio State University Comprehensive Cancer CenterColumbusOhioUSA
| | | | - Federica Calore
- Department of Cancer Biology and GeneticsThe Ohio State UniversityColumbusOhioUSA
| | - Giovanni Nigita
- Department of Cancer Biology and GeneticsThe Ohio State UniversityColumbusOhioUSA
| | - Sayumi Tahara
- The Ohio State University Comprehensive Cancer CenterColumbusOhioUSA
| | - Luciano Cascione
- Institute of Oncology Research (IOR), Faculty of Biomedical SciencesUniversità della Svizzera italiana (USI), Bellinzona, Switzerland, Swiss Institute of Bioinformatics (SIB)LausanneSwitzerland
| | - Martin Wabitsch
- Department of Pediatrics and Adolescent Medicine Division of Paediatric Endocrinology and Diabetes Centre for Hormonal Disorders in Children and AdolescentsUlm University HospitalUlmGermany
| | - Francis J. Hornicek
- Sarcoma Biology Laboratory, Department of Orthopaedics, Sylvester Comprehensive Cancer Centerand the University of Miami Miller School of MedicineMiamiFloridaUSA
| | - Valerie Grignol
- The Ohio State University Comprehensive Cancer CenterColumbusOhioUSA
| | - Carlo M. Croce
- Department of Cancer Biology and GeneticsThe Ohio State UniversityColumbusOhioUSA
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Barreca M, Spanò V, Rocca R, Bivacqua R, Abel AC, Maruca A, Montalbano A, Raimondi MV, Tarantelli C, Gaudio E, Cascione L, Rinaldi A, Bai R, Steinmetz M, Prota A, Alcaro S, Hamel E, Bertoni F, Barraja P. Development of [1,2]oxazoloisoindoles tubulin polymerization inhibitors: Further chemical modifications and potential therapeutic effects against lymphomas. Eur J Med Chem 2022; 243:114744. [DOI: 10.1016/j.ejmech.2022.114744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/18/2022] [Accepted: 09/03/2022] [Indexed: 11/04/2022]
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Spriano F, Sartori G, Tarantelli C, Barreca M, Golino G, Rinaldi A, Napoli S, Mascia M, Scalise L, Arribas AJ, Cascione L, Zucca E, Stathis A, Gaudio E, Bertoni F. Pharmacologic screen identifies active combinations with BET inhibitors and LRRK2 as a novel putative target in lymphoma. eJHaem 2022; 3:764-774. [PMID: 36051080 PMCID: PMC9422027 DOI: 10.1002/jha2.535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/05/2022] [Accepted: 07/08/2022] [Indexed: 11/26/2022]
Abstract
Inhibitors of the Bromo‐ and Extra‐Terminal domain (BET) family proteins have strong preclinical antitumor activity in multiple tumor models, including lymphomas. Limited single‐agent activity has been reported in the clinical setting. Here, we have performed a pharmacological screening to identify compounds that can increase the antitumor activity of BET inhibitors in lymphomas. The germinal center B‐cell like diffuse large B‐cell lymphoma (DLBCL) cell lines OCI‐LY‐19 and WSU‐DLCL2 were exposed to 348 compounds given as single agents at two different concentrations and in combination with the BET inhibitor birabresib. The combination partners included small molecules targeting important biologic pathways such as PI3K/AKT/MAPK signaling and apoptosis, approved anticancer agents, kinase inhibitors, epigenetic compounds. The screening identified a series of compounds leading to a stronger antiproliferative activity when given in combination than as single agents: the histone deacetylase (HDAC) inhibitors panobinostat and dacinostat, the mTOR (mechanistic target of rapamycin) inhibitor everolimus, the ABL/SRC (ABL proto‐oncogene/SRC proto oncogene) inhibitor dasatinib, the AKT1/2/3 inhibitor MK‐2206, the JAK2 inhibitor TG101209. The novel finding was the benefit given by the addition of the LRRK2 inhibitor LRRK2‐IN‐1, which was validated in vitro and in vivo. Genetic silencing demonstrated that LRRK2 sustains the proliferation of lymphoma cells, a finding paired with the association between high expression levels and inferior outcome in DLBCL patients. We identified combinations that can improve the response to BET inhibitors in lymphomas, and LRRK2 as a gene essential for lymphomas and as putative novel target for this type of tumors.
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Affiliation(s)
- Filippo Spriano
- Institute of Oncology Research Faculty of Biomedical Sciences Università della Svizzera Italiana Bellinzona Switzerland
| | - Giulio Sartori
- Institute of Oncology Research Faculty of Biomedical Sciences Università della Svizzera Italiana Bellinzona Switzerland
| | - Chiara Tarantelli
- Institute of Oncology Research Faculty of Biomedical Sciences Università della Svizzera Italiana Bellinzona Switzerland
| | - Marilia Barreca
- Institute of Oncology Research Faculty of Biomedical Sciences Università della Svizzera Italiana Bellinzona Switzerland
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF) University of Palermo Palermo Italy
| | - Gaetanina Golino
- Institute of Oncology Research Faculty of Biomedical Sciences Università della Svizzera Italiana Bellinzona Switzerland
| | - Andrea Rinaldi
- Institute of Oncology Research Faculty of Biomedical Sciences Università della Svizzera Italiana Bellinzona Switzerland
| | - Sara Napoli
- Institute of Oncology Research Faculty of Biomedical Sciences Università della Svizzera Italiana Bellinzona Switzerland
| | - Michele Mascia
- Institute of Oncology Research Faculty of Biomedical Sciences Università della Svizzera Italiana Bellinzona Switzerland
| | - Lorenzo Scalise
- Institute of Oncology Research Faculty of Biomedical Sciences Università della Svizzera Italiana Bellinzona Switzerland
| | - Alberto J. Arribas
- Institute of Oncology Research Faculty of Biomedical Sciences Università della Svizzera Italiana Bellinzona Switzerland
- SIB Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Luciano Cascione
- Institute of Oncology Research Faculty of Biomedical Sciences Università della Svizzera Italiana Bellinzona Switzerland
- SIB Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Emanuele Zucca
- Institute of Oncology Research Faculty of Biomedical Sciences Università della Svizzera Italiana Bellinzona Switzerland
- Department of Oncology Oncology Institute of Southern Switzerland Ente Ospedaliero Cantonale Bellinzona Switzerland
| | - Anastasios Stathis
- Department of Oncology Oncology Institute of Southern Switzerland Ente Ospedaliero Cantonale Bellinzona Switzerland
- Faculty of Biomedical Sciences Università della Svizzera Italiana Lugano Switzerland
| | - Eugenio Gaudio
- Institute of Oncology Research Faculty of Biomedical Sciences Università della Svizzera Italiana Bellinzona Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research Faculty of Biomedical Sciences Università della Svizzera Italiana Bellinzona Switzerland
- Department of Oncology Oncology Institute of Southern Switzerland Ente Ospedaliero Cantonale Bellinzona Switzerland
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Chilà R, Chiappa M, Guffanti F, Panini N, Conconi D, Rinaldi A, Cascione L, Bertoni F, Fratelli M, Damia G. Stable CDK12 Knock-Out Ovarian Cancer Cells Do Not Show Increased Sensitivity to Cisplatin and PARP Inhibitor Treatment. Front Oncol 2022; 12:903536. [PMID: 35912188 PMCID: PMC9328802 DOI: 10.3389/fonc.2022.903536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/24/2022] [Indexed: 11/23/2022] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) is a serine/threonine kinase involved in the regulation of RNA polymerase II and in the transcription of a subset of genes involved in the DNA damage response. CDK12 is one of the most mutated genes in ovarian carcinoma. These mutations result in loss-of-function and can predict the responses to PARP1/2 inhibitor and platinum. To investigate the role of CDK12 in ovarian cancer, CRISPR/Cas9 technology was used to generate a stable CDK12 knockout (KO) clone in A2780 ovarian carcinoma cells. This is the first report on a CDK12 null cell line. The clone had slower cell growth and was less clonogenic than parental cells. These data were confirmed in vivo, where CDK12 KO transplanted cells had a much longer time lag and slightly slower growth rate than CDK12-expressing cells. The slower growth was associated with a higher basal level of apoptosis, but there were no differences in the basal level of autophagy and senescence. While cell cycle distribution was similar in parental and knockout cells, there was a doubling in DNA content, with an almost double modal number of chromosomes in the CDK12 KO clone which, however did not display any increase in γH2AX, a marker of DNA damage. We found partial down-regulation of the expression of DNA repair genes at the mRNA level and, among the down-regulated genes, an enrichment in the G2/M checkpoint genes. Although the biological features of CDK12 KO cells are compatible with the function of CDK12, contrary to some reports, we could not find any difference in the sensitivity to cisplatin and olaparib between wild-type and CDK12 KO cells.
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Affiliation(s)
- Rosaria Chilà
- Laboratory of Experimental Oncology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri Istituito di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Michela Chiappa
- Laboratory of Experimental Oncology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri Istituito di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Federica Guffanti
- Laboratory of Experimental Oncology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri Istituito di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Nicolò Panini
- Laboratory of Cancer Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Donatella Conconi
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Andrea Rinaldi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland
| | - Maddalena Fratelli
- Department of Biochemistry, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Giovanna Damia
- Laboratory of Experimental Oncology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri Istituito di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
- *Correspondence: Giovanna Damia,
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Mensah AA, Valente S, Matkovic M, Sartori G, Falzarano C, Tarantelli C, Cascione L, Pileri SA, Cavalli A, Mai A, Bertoni F. Abstract 3279: Dual inhibition of EZH2 and histone deacetylases for the treatment of lymphomas with epigenetic aberrations. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3279] [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: Lymphomas are characterized by aberrations in epigenetic proteins that contribute to establishing and maintaining the malignant phenotype. Gain of function mutations in EZH2 histone methyltransferase and inactivating mutations in CREBBP acetyltransferase occur in up to 30% of diffuse large B cell lymphomas (DLBCLs). Half of DLBCLs with mutated EZH2 have also mutated CREBBP. In vitro, mutated EZH2 DLBCLs have a lower sensitivity to HDAC inhibitors, HDACi (Mensah et al, 2021). Here, we explored the dual pharmacological inhibition of EZH2 and HDAC for an improved anti-lymphoma activity.
Methods: Biochemical evaluation and characterization of target engagement were done using fluorescence polarization, thermal shift, surface plasmon resonance, isothermal titration calorimetry and microscale thermophoresis. Computer modelling was performed using available EZH2 and HDACs crystal structures. Anti-proliferative activity was assessed after 7 days (d) using MTT and live imaging in DLBCL cells (n = 5). For cell cycle analysis by flow cytometry, cells were treated, fixed then stained with 7-AAD.
Results: We designed and synthesized 2 dual EZH2/HDAC inhibitors, MC4343 and MC4355, starting from the structures of EZH2 inhibitor tazemetostat (taz) and HDACi vorinostat. In biochemical assays, MC4343 and MC4355 had equal potencies towards EZH2 (0.032 nM) but different specificities towards class I and class II HDACs: MC4355 showed 7.5-fold greater inhibition of HDAC3 compared to MC4343 (0.38 µM and 2.85 µM, respectively) and more potently inhibited HDACs 6 and 8 (0.016, 0.17 µM and no activity, respectively). Computational modelling showed that the coordinative functional group of MC4343, but not of MC4355, caused steric clashes with several HDACs in increasing order: HDAC1 = HDAC3 > HDAC8 >> HDAC4 = HDAC6. These results closely mirrored those obtained from the biochemical analysis. Both compounds inhibited proliferation in DLBCL cell lines irrespective of EZH2 or CREBBP mutational status but EZH2 and/or CREBBP mutants were more sensitive. MC4355 (IC50 range = 0.17 - 1.68 µM; median = 0.2 µM) was more potent than MC4343 (IC50 range = 0.17-2.72 µM; median = 1.78 µM). This was confirmed by live imaging analyses. SUDHL4, with EZH2 Y666N, showed poorer sensitivity to both inhibitors compared to DLBCLs with EZH2 Y646N/S. MC4343 and MC4355 induced cell death and G1 arrest in a dose-dependent manner. Pfeiffer, KARPAS422, WSUDLCL2, most sensitive to taz alone (IC50 = 4, 16, 77 nM), were most sensitive to MC4355 (IC50 = 200, 174, 171 nM). Notably, dual inhibitor treatment of Toledo and SUDHL4 with low sensitivity to taz (IC50 = 9, 14 µM), partially rescued sensitivity (IC50 = 1.7, 1.6 µM).
Conclusions: We designed and synthesized 2 novel dual EZH2/HDAC inhibitors, MC4343 and MC4355, with robust anti-proliferative effects in DLBCL. Our data show the efficacy of this novel class of epigenetic agents in lymphomas.
Citation Format: Afua Adjeiwaa Mensah, Sergio Valente, Milos Matkovic, Giulio Sartori, Chiara Falzarano, Chiara Tarantelli, Luciano Cascione, Stefano A. Pileri, Andrea Cavalli, Antonello Mai, Francesco Bertoni. Dual inhibition of EZH2 and histone deacetylases for the treatment of lymphomas with epigenetic aberrations [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 3279.
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Affiliation(s)
- Afua Adjeiwaa Mensah
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | | | - Milos Matkovic
- 3Institute for Research in Biomedicine, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Giulio Sartori
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Chiara Falzarano
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Chiara Tarantelli
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Luciano Cascione
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Stefano A. Pileri
- 4Division of Diagnostic Haematopathology, European Institute of Oncology, Milan, Italy
| | - Andrea Cavalli
- 3Institute for Research in Biomedicine, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | | | - Francesco Bertoni
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
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Sartori G, Cascione L, Matkovic M, Matsunami H, Cavalli A, Bertoni F. Abstract 2655: The GPCR OR13A1 is essential for lymphoma cells. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2655] [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. G protein-coupled receptors (GPCRs) are integral membrane proteins that mediate cellular responses to endogenous (amines, cations, lipids, peptides, glycoproteins) and exogenous (light, tastants, odorants) stimuli. Altered signaling pathways associated with GPCRs are implicated in the pathophysiology of various diseases, such as CXCR3/4/5, S1PR1/2/3, GPR34 in lymphomas. Olfactory receptors (ORs) are GPCRs, initially identified and characterized for their expression in olfactory neurons but now recognized as expressed in different tissues. OR51E1 is known as prostate specific G protein coupled receptor 2 (PSGR2) due to its expression in prostate cancer, OR2B6 and OR2W3 are expressed in breast cancer, and OR51E1 in melanoma. OR13A1 has been included in the double-hit expression signature reported in diffuse large B cell lymphoma (DLBCL) (Ennishi et al 2019). Here, we studied OR13A1 in lymphoma cell lines and clinical specimens.
Methods. RNA-Seq and real-time PCR for evaluating the expression of ORs in DLBCL cell lines. Gene expression data for clinical samples obtained from public dataset phs001444.v2.p1. OR13A1 silencing performed with both siRNAs (OCI-Ly1, U2932) and doxycycline-inducible shRNAs (U2932); viability assessed after 3 days using MTT and for longer with Incucyte live imaging. Computer modelling performed based on available ligands for the murine orthologue Olfr211 and similar known GPCRs structure.
Results. Only one OR per cell line was usually expressed, as reported for olfactory cells. Using RNA-Seq and real-time PCR, OR13A1 gene appeared the most abundantly expressed in lymphomas cell lines compared to others ORs. Its expression was seen in 35/47 B cell lymphoma lines, with higher expression in germinal center B cell (GCB) DLBCL than activated B cell like (ABC) DLBCL (P 0.03). A similar pattern was observed in patients: higher expression in GCB than ABC and in EZB than MCD (P < 0.001). OR13A1 also appeared higher in normal GC cells than in naïve and memory B cells. Among GCB DLBCL patients, OR13A1 expression was associated with inferior outcome. Silencing of OR13A1 with siRNAs in GCB and ABC DLBCL cells caused > 50% reduction in cell viability, and pERK downregulation. Viability data were confirmed using a doxycycline-inducible shRNA system and live cell imaging instrument. Natural compounds reported as ligands for the murine orthologue Olfr211 or in silico identified to bind as agonists (ex: tyramine) increased cell line growth and compounds predicted to bind as antagonists (ex: cyclohexanone) decreased the cell viability in the presence but not in the absence of the GPCR.
Conclusion. OR13A1 gene appeared more abundantly expressed in lymphomas compared to others ORs, higher in GCB than ABC DLBCL and with a possible impact on clinical outcome. Genetic and chemical experiments showed that this GPCR has an essential function in lymphoma cells and could represent a novel therapeutic target.
Citation Format: Giulio Sartori, Luciano Cascione, Milos Matkovic, Hiroaki Matsunami, Andrea Cavalli, Francesco Bertoni. The GPCR OR13A1 is essential for lymphoma cells [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 2655.
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Affiliation(s)
- Giulio Sartori
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Luciano Cascione
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Milos Matkovic
- 2Institute for Research in Biomedicine, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Hiroaki Matsunami
- 3Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC
| | - Andrea Cavalli
- 2Institute for Research in Biomedicine, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Francesco Bertoni
- 1Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
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28
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Arribas AJ, Napoli S, Cascione L, Sartori G, Barnabei L, Gaudio E, Tarantelli C, Mensah AA, Spriano F, Zucchetto A, Rossi FM, Rinaldi A, De Moura MC, Jovic S, Bordone-Pittau R, Di Veroli A, Stathis A, Cruciani G, Stussi G, Gattei V, Brown JR, Esteller M, Zucca E, Rossi D, Bertoni F. Resistance to PI3κδ inhibitors in marginal zone lymphoma can be reverted by targeting the IL-6/PDGFRA axis. Haematologica 2022; 107:2685-2697. [PMID: 35484662 PMCID: PMC9614536 DOI: 10.3324/haematol.2021.279957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Indexed: 11/24/2022] Open
Abstract
PI3Kδ inhibitors are active in patients with lymphoid neoplasms and a first series of them have been approved for the treatment of multiple types of B-cell lymphoid tumors, including marginal zone lymphoma (MZL). The identification of the mechanisms underlying either primary or secondary resistance is fundamental to optimize the use of novel drugs. Here we present a model of secondary resistance to PI3Kδ inhibitors obtained by prolonged exposure of a splenic MZL cell line to idelalisib. The VL51 cell line was kept under continuous exposure to idelalisib. The study included detailed characterization of the model, pharmacological screens, silencing experiments, and validation experiments on multiple cell lines and on clinical specimens. VL51 developed resistance to idelalisib, copanlisib, duvelisib, and umbralisib. An integrative analysis of transcriptome and methylation data highlighted an enrichment of upregulated transcripts and low-methylated promoters in resistant cells, including IL-6/STAT3- and PDGFRA-related genes and surface CD19 expression, alongside the repression of the let-7 family of miRNA, and miR-125, miR-130, miR-193 and miR-20. The IL-6R blocking antibody to-cilizumab, the STAT3 inhibitor stattic, the LIN28 inhibitor LIN1632, the PDGFR inhibitor masitinib and the anti-CD19 antibody drug conjugate loncastuximab tesirine were active compounds in the resistant cells as single agents and/or in combination with PI3Kδ inhibition. Findings were validated on additional in vitro lymphoma models and on clinical specimens. A novel model of resistance obtained from splenic MZL allowed the identification of therapeutic approaches able to improve the antitumor activity of PI3Kδ inhibitors in B-cell lymphoid tumors.
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Affiliation(s)
- Alberto J Arribas
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne.
| | - Sara Napoli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne
| | - Giulio Sartori
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona
| | - Laura Barnabei
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona
| | - Eugenio Gaudio
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona
| | - Chiara Tarantelli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona
| | | | - Filippo Spriano
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona
| | | | | | - Andrea Rinaldi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona
| | | | - Sandra Jovic
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona
| | | | - Alessandra Di Veroli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia
| | - Anastasios Stathis
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland; Faculty of Biomedical Sciences, USI, Bellinzona
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia
| | - Georg Stussi
- Oncology Institute of Southern Switzerland, Bellinzona
| | - Valter Gattei
- Centro di Riferimento Oncologico di Aviano - CRO, Aviano
| | - Jennifer R Brown
- Chronic Lymphocytic Leukemia Center, Division of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia
| | - Emanuele Zucca
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland; Oncology Institute of Southern Switzerland, Bellinzona
| | - Davide Rossi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland; Oncology Institute of Southern Switzerland, Bellinzona
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland; Oncology Institute of Southern Switzerland, Bellinzona.
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Galuppini F, Censi S, Merante Boschin I, Fassan M, Sbaraglia M, Valeri N, Hahne JC, Bertazza L, Munari G, Galasso M, Cascione L, Barollo S, Rugge M, Vianello F, Dei Tos AP, Mian C, Pennelli G. Papillary Thyroid Carcinoma: Molecular Distinction by MicroRNA Profiling. Front Endocrinol (Lausanne) 2022; 13:834075. [PMID: 35282462 PMCID: PMC8904882 DOI: 10.3389/fendo.2022.834075] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/26/2022] [Indexed: 12/15/2022] Open
Abstract
Papillary thyroid carcinoma (PTC) is a miscellaneous disease with a variety of histological variants, each with its own mutational profile, and clinical and prognostic characteristics. Identification of microRNA (miRNA) expression profiles represents an important benchmark for understanding the molecular mechanisms underlying the biological behavior of these unique PTC subtypes in order that they be better characterized. We considered a series of 35 PTC samples with a histological diagnosis of either hobnail (17 cases) or classical variant (nine cases) and with a specific BRAF p.K601E mutation (nine cases). We determined the overall miRNA expression profile with NanoString technology, and both quantitative reverse transcription-PCR and in situ hybridization were used to confirm selected miRNAs. The miRNA signature was found to consistently differentiate specific histotypes and mutational profiles. In contrast to the BRAF p.K601E mutation and classic PTCs, three miRNAs (miR-21-5p, miR-146b-5p, and miR-205-5p) were substantially overexpressed in the hobnail variant. The current study found that different miRNA signature profiles were linked to unique histological variants and BRAF mutations in PTC. Further studies focusing on the downstream pathogenetic functions of mRNAs in thyroid neoplasms are warranted.
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Affiliation(s)
- Francesca Galuppini
- Pathology Unit, Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Simona Censi
- Endocrinology Unit, Department of Medicine (DIMED), University of Padua, Padua, Italy
| | | | - Matteo Fassan
- Pathology Unit, Department of Medicine (DIMED), University of Padua, Padua, Italy
- Veneto Institute of Oncology, Istituto Di Ricovero E Cura a Carattere Scientifico (IRCCS), Padua, Italy
| | - Marta Sbaraglia
- Pathology Unit, Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Nicola Valeri
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Jens Claus Hahne
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Loris Bertazza
- Endocrinology Unit, Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Giada Munari
- Pathology Unit, Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Marco Galasso
- Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Luciano Cascione
- Bioinformatics Core Unit, Institute of Oncology Research, Bellinzona, Switzerland
| | - Susi Barollo
- Endocrinology Unit, Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Massimo Rugge
- Pathology Unit, Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Federica Vianello
- Department of Radiotherapy, Veneto Institute of Oncology, Istituto Di Ricovero E Cura a Carattere Scientifico (IRCCS), Padua, Italy
| | - Angelo Paolo Dei Tos
- Pathology Unit, Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Caterina Mian
- Endocrinology Unit, Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Gianmaria Pennelli
- Pathology Unit, Department of Medicine (DIMED), University of Padua, Padua, Italy
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30
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Genta S, Ghilardi G, Cascione L, Juskevicius D, Tzankov A, Schär S, Milan L, Pirosa MC, Esposito F, Ruberto T, Giovanella L, Hayoz S, Mamot C, Dirnhofer S, Zucca E, Ceriani L. Integration of Baseline Metabolic Parameters and Mutational Profiles Predicts Long-Term Response to First-Line Therapy in DLBCL Patients: A Post Hoc Analysis of the SAKK38/07 Study. Cancers (Basel) 2022; 14:cancers14041018. [PMID: 35205765 PMCID: PMC8870624 DOI: 10.3390/cancers14041018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 12/16/2022] Open
Abstract
Accurate estimation of the progression risk after first-line therapy represents an unmet clinical need in diffuse large B-cell lymphoma (DLBCL). Baseline (18)F-fluorodeoxyglucose positron emission tomography/computed tomography (PET/CT) parameters, together with genetic analysis of lymphoma cells, could refine the prediction of treatment failure. We evaluated the combined impact of mutation profiling and baseline PET/CT functional parameters on the outcome of DLBCL patients treated with the R-CHOP14 regimen in the SAKK38/07 clinical trial (NCT00544219). The concomitant presence of mutated SOCS1 with wild-type CREBBP and EP300 defined a group of patients with a favorable prognosis and 2-year progression-free survival (PFS) of 100%. Using an unsupervised recursive partitioning approach, we generated a classification-tree algorithm that predicts treatment outcomes. Patients with elevated metabolic tumor volume (MTV) and high metabolic heterogeneity (MH) (15%) had the highest risk of relapse. Patients with low MTV and favorable mutational profile (9%) had the lowest risk, while the remaining patients constituted the intermediate-risk group (76%). The resulting model stratified patients among three groups with 2-year PFS of 100%, 82%, and 42%, respectively (p < 0.001).
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Affiliation(s)
- Sofia Genta
- Clinic of Medical Oncology, Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland; (S.G.); (M.C.P.); (F.E.); (E.Z.)
| | - Guido Ghilardi
- Clinic of Hematology, Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland;
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland;
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Darius Juskevicius
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland; (D.J.); (A.T.); (S.D.)
| | - Alexandar Tzankov
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland; (D.J.); (A.T.); (S.D.)
| | - Sämi Schär
- Swiss Group for Clinical Cancer Research (SAKK) Coordinating Center, 3008 Bern, Switzerland; (S.S.); (S.H.)
| | - Lisa Milan
- Clinic of Nuclear Medicine and PET/CT Center, Imaging Institute of Southern Switzerland, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland; (L.M.); (T.R.); (L.G.)
| | - Maria Cristina Pirosa
- Clinic of Medical Oncology, Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland; (S.G.); (M.C.P.); (F.E.); (E.Z.)
- Clinic of Hematology, Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland;
| | - Fabiana Esposito
- Clinic of Medical Oncology, Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland; (S.G.); (M.C.P.); (F.E.); (E.Z.)
| | - Teresa Ruberto
- Clinic of Nuclear Medicine and PET/CT Center, Imaging Institute of Southern Switzerland, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland; (L.M.); (T.R.); (L.G.)
| | - Luca Giovanella
- Clinic of Nuclear Medicine and PET/CT Center, Imaging Institute of Southern Switzerland, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland; (L.M.); (T.R.); (L.G.)
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, 8006 Zurich, Switzerland
| | - Stefanie Hayoz
- Swiss Group for Clinical Cancer Research (SAKK) Coordinating Center, 3008 Bern, Switzerland; (S.S.); (S.H.)
| | - Christoph Mamot
- Division of Oncology, Cantonal Hospital Aarau, 5001 Aarau, Switzerland;
| | - Stefan Dirnhofer
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland; (D.J.); (A.T.); (S.D.)
| | - Emanuele Zucca
- Clinic of Medical Oncology, Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland; (S.G.); (M.C.P.); (F.E.); (E.Z.)
- Institute of Oncology Research, Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland;
- Department of Medical Oncology, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Luca Ceriani
- Institute of Oncology Research, Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland;
- Clinic of Nuclear Medicine and PET/CT Center, Imaging Institute of Southern Switzerland, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland; (L.M.); (T.R.); (L.G.)
- Correspondence:
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31
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Bonfiglio F, Bruscaggin A, Guidetti F, Terzi di Bergamo L, Faderl M, Spina V, Condoluci A, Bonomini L, Forestieri G, Koch R, Piffaretti D, Pini K, Pirosa MC, Cittone MG, Arribas A, Lucioni M, Ghilardi G, Wu W, Arcaini L, Baptista MJ, Bastidas G, Bea S, Boldorini R, Broccoli A, Buehler MM, Canzonieri V, Cascione L, Ceriani L, Cogliatti S, Corradini P, Derenzini E, Devizzi L, Dietrich S, Elia AR, Facchetti F, Gaidano G, Garcia JF, Gerber B, Ghia P, Gomes da Silva M, Gritti G, Guidetti A, Hitz F, Inghirami G, Ladetto M, Lopez-Guillermo A, Lucchini E, Maiorana A, Marasca R, Matutes E, Meignin V, Merli M, Moccia A, Mollejo M, Montalban C, Novak U, Oscier DG, Passamonti F, Piazza F, Pizzolitto S, Rambaldi A, Sabattini E, Salles G, Santambrogio E, Scarfò L, Stathis A, Stüssi G, Geyer JT, Tapia G, Tarella C, Thieblemont C, Tousseyn T, Tucci A, Vanini G, Visco C, Vitolo U, Walewska R, Zaja F, Zenz T, Zinzani PL, Khiabanian H, Calcinotto A, Bertoni F, Bhagat G, Campo E, De Leval L, Dirnhofer S, Pileri SA, Piris MA, Traverse-Glehen A, Tzankov A, Paulli M, Ponzoni M, Mazzucchelli L, Cavalli F, Zucca E, Rossi D. Genetic and phenotypic attributes of splenic marginal zone lymphoma. Blood 2022; 139:732-747. [PMID: 34653238 DOI: 10.1182/blood.2021012386] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/14/2021] [Indexed: 11/20/2022] Open
Abstract
Splenic marginal zone B-cell lymphoma (SMZL) is a heterogeneous clinico-biological entity. The clinical course is variable, multiple genes are mutated with no unifying mechanism, and essential regulatory pathways and surrounding microenvironments are diverse. We sought to clarify the heterogeneity of SMZL by resolving different subgroups and their underlying genomic abnormalities, pathway signatures, and microenvironment compositions to uncover biomarkers and therapeutic vulnerabilities. We studied 303 SMZL spleen samples collected through the IELSG46 multicenter international study (NCT02945319) by using a multiplatform approach. We carried out genetic and phenotypic analyses, defined self-organized signatures, validated the findings in independent primary tumor metadata and in genetically modified mouse models, and determined correlations with outcome data. We identified 2 prominent genetic clusters in SMZL, termed NNK (58% of cases, harboring NF-κB, NOTCH, and KLF2 modules) and DMT (32% of cases, with DNA-damage response, MAPK, and TLR modules). Genetic aberrations in multiple genes as well as cytogenetic and immunogenetic features distinguished NNK- from DMT-SMZLs. These genetic clusters not only have distinct underpinning biology, as judged by differences in gene-expression signatures, but also different outcomes, with inferior survival in NNK-SMZLs. Digital cytometry and in situ profiling segregated 2 basic types of SMZL immune microenvironments termed immune-suppressive SMZL (50% of cases, associated with inflammatory cells and immune checkpoint activation) and immune-silent SMZL (50% of cases, associated with an immune-excluded phenotype) with distinct mutational and clinical connotations. In summary, we propose a nosology of SMZL that can implement its classification and also aid in the development of rationally targeted treatments.
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Affiliation(s)
- Ferdinando Bonfiglio
- Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland
| | - Alessio Bruscaggin
- Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland
| | - Francesca Guidetti
- Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland
| | | | - Martin Faderl
- Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland
| | - Valeria Spina
- Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland
| | - Adalgisa Condoluci
- Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland
- Division of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Luisella Bonomini
- International Extranodal Lymphoma Study Group, Bellinzona, Switzerland
| | - Gabriela Forestieri
- Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland
| | - Ricardo Koch
- Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland
| | - Deborah Piffaretti
- Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland
| | - Katia Pini
- Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland
| | - Maria Cristina Pirosa
- Division of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Micol Giulia Cittone
- Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland
- Division of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Alberto Arribas
- Lymphoma Genomics, Institute of Oncology Research, Bellinzona, Switzerland
| | - Marco Lucioni
- Unit of Anatomic Pathology, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and Università degli Studi di Pavia, Pavia, Italy
| | - Guido Ghilardi
- Division of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Wei Wu
- Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland
| | - Luca Arcaini
- Division of Hematology, Fondazione IRCCS Policlinico San Matteo and Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Maria Joao Baptista
- Lymphoid Neoplasms Group, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - Gabriela Bastidas
- Division of Hematology, Hospital Clínic i Provincial de Barcelona, Barcelona, Spain
| | - Silvia Bea
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) 28029, Madrid, Spain
- Pathology Department, Hospital Clínic, Barcelona University, Barcelona, Spain
| | - Renzo Boldorini
- Division of Pathology, University of Eastern Piedmont, Novara, Italy
| | - Alessandro Broccoli
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia Seràgnoli, Bologna, Italy
| | - Marco Matteo Buehler
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Vincenzo Canzonieri
- Pathology Unit, CRO Aviano National Cancer Institute, Aviano, Italy
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Luciano Cascione
- Lymphoma Genomics, Institute of Oncology Research, Bellinzona, Switzerland
| | - Luca Ceriani
- Clinic of Nuclear Medicine and PET-CT Centre, Imaging Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Sergio Cogliatti
- Institute of Pathology, Kantonsspital St Gallen, St Gallen, Switzerland
| | - Paolo Corradini
- Division of Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Enrico Derenzini
- Onco-hematology Division, European Institute of Oncology (IEO) IRCCS, Milan, Italy
| | - Liliana Devizzi
- Division of Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Sascha Dietrich
- Division of Hematology, University Hospital Heidelberg, Heidelberg, Germany
| | - Angela Rita Elia
- Cancer Immunotherapy, Institute of Oncology Research, Bellinzona, Switzerland
| | - Fabio Facchetti
- Department of Molecular and Translational Medicine, Pathology Unit, Spedali Civili, Brescia, Italy
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | | | - Bernhard Gerber
- Division of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Department of Hematology and Oncology, University of Zurich, Zurich, Switzerland
| | - Paolo Ghia
- Strategic Research Program on Chronic Lymphocytic Leukemia (CLL), IRCCS Ospedale San Raffaele and Università Vita-Salute San Raffaele, Milan, Italy
| | - Maria Gomes da Silva
- Division of Hematology, Instituto Português de Oncologia de Lisboa, Lisbon, Portugal
| | - Giuseppe Gritti
- Division of Hematology, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy
| | - Anna Guidetti
- Division of Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Felicitas Hitz
- Division of Hematology, Kantonsspital St Gallen, St Gallen, Switzerland
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Marco Ladetto
- Division of Hematology, Azienda Ospedaliera SS Antonio e Biagio, Alessandria, Italy
- Dipartimento di Medicina Traslazionale, University of Eastern Piedmont, Alessandria, Italy
| | | | - Elisa Lucchini
- Division of Hematology, Azienda Sanitaria Universitaria Giuliano Isontina, Trieste, Italy
| | - Antonino Maiorana
- Division of Pathology, Universitá degli Studi di Modena e Reggio Emilia, Modena, Italy
| | - Roberto Marasca
- Hematology Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Estella Matutes
- Haematopathology Unit, Hospital Clínic i Provincial de Barcelona, Barcelona, Spain
| | | | - Michele Merli
- Division of Hematology, University of Insubria and ASST Sette Laghi, Ospedale di Circolo of Varese, Varese, Italy
| | - Alden Moccia
- Clinic of Medical Oncology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Manuela Mollejo
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) 28029, Madrid, Spain
- Division of Pathology, Hospital Virgen de la Salud, Toledo, Spain
| | - Carlos Montalban
- Division of Hematology, MD Anderson Cancer Center, Madrid, Spain
| | - Urban Novak
- Department of Medical Oncology and University Cancer Center, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - David Graham Oscier
- Division of Hematology, University Hospitals Dorset, Bournemouth, United Kingdom
| | - Francesco Passamonti
- Department of Medicine and Surgery, University of Insubria and ASST Sette Laghi, Ospedale di Circolo of Varese, Varese, Italy
| | - Francesco Piazza
- Division of Hematology, Ospedale Universitario di Padova, Padova, Italy
| | - Stefano Pizzolitto
- Division of Pathology, General Hospital S Maria della Misericordia, Udine, Italy
| | - Alessandro Rambaldi
- Division of Hematology, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy
| | - Elena Sabattini
- Haematopathology Unit, Department of Experimental Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Gilles Salles
- Faculté de Médecine et de Maïeutique Lyon Sud, Université de Lyon, Lyon, France
| | | | - Lydia Scarfò
- Strategic Research Program on Chronic Lymphocytic Leukemia (CLL), IRCCS Ospedale San Raffaele and Università Vita-Salute San Raffaele, Milan, Italy
| | - Anastasios Stathis
- Clinic of Medical Oncology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Georg Stüssi
- Division of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Lugano, Switzerland
| | - Julia T Geyer
- Division of Anatomic Pathology and Clinical Pathology, Weill Cornell Medical College, New York, NY
| | - Gustavo Tapia
- Division of Pathology, Hospital Germans Trias I Pujol, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Corrado Tarella
- Onco-hematology Division, European Institute of Oncology (IEO) IRCCS, Milan, Italy
| | - Catherine Thieblemont
- Assistance Publique-Hôpitaux de Paris, Hopital Saint-Louis, Hemato-Oncology Unit; Université de Paris, Paris, France
| | - Thomas Tousseyn
- Department of Haematology, University Hospitals Leuven, Leuven, Belgium
| | | | - Giorgio Vanini
- Department of Medical Oncology and University Cancer Center, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Carlo Visco
- Department of Medicine, Section of Hematology, University of Verona, Italy
| | - Umberto Vitolo
- Candiolo Cancer Institute (FPO-IRCCS), Candiolo, Turin, Italy
| | - Renata Walewska
- Division of Hematology, University Hospitals Dorset, Bournemouth, United Kingdom
| | - Francesco Zaja
- Division of Hematology, Azienda Sanitaria Universitaria Giuliano Isontina, Trieste, Italy
| | - Thorsten Zenz
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Pier Luigi Zinzani
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia Seràgnoli, Bologna, Italy
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Università di Bologna, Bologna, Italy
| | - Hossein Khiabanian
- Center for Systems and Computational Biology, Rutgers University, New Brunswick, NJ
| | - Arianna Calcinotto
- Cancer Immunotherapy, Institute of Oncology Research, Bellinzona, Switzerland
| | - Francesco Bertoni
- Lymphoma Genomics, Institute of Oncology Research, Bellinzona, Switzerland
- Clinic of Medical Oncology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Lugano, Switzerland
| | - Govind Bhagat
- Department of Pathology and Cell Biology, Columbia University, New York, NY
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS)
- Pathology Department, Hospital Clínic, Barcelona University, Barcelona, Spain
| | - Laurence De Leval
- Division of Pathology, Institut Universitaire de Pathologie, Lausanne, Switzerland
| | - Stefan Dirnhofer
- Institute of Pathology and Medical Genetics, University Hospital Basel, Basel, Switzerland
| | - Stefano A Pileri
- Haematopathology Division, European Institute of Oncology IRCCS, Milan, Italy
| | - Miguel A Piris
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) 28029, Madrid, Spain
- Pathology Service, Fundación Jiménez Díaz, Madrid, Spain
| | | | - Alexander Tzankov
- Institute of Pathology and Medical Genetics, University Hospital Basel, Basel, Switzerland
| | - Marco Paulli
- Unit of Anatomic Pathology, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and Università degli Studi di Pavia, Pavia, Italy
| | - Maurilio Ponzoni
- Ateneo Vita-Salute San Raffaele University and Pathology Unit San Raffaele Scientific Institute, Milan, Italy
| | - Luca Mazzucchelli
- Division of Pathology, Cantonal Institute of Pathology, Locarno, Switzerland
| | - Franco Cavalli
- Institute of Oncology Research, Bellinzona, Switzerland; and
| | - Emanuele Zucca
- International Extranodal Lymphoma Study Group, Bellinzona, Switzerland
- Clinic of Medical Oncology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Lugano, Switzerland
- Department of Medical Oncology, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Davide Rossi
- Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland
- Division of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Lugano, Switzerland
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Terzi di Bergamo L, Guidetti F, Rossi D, Bertoni F, Cascione L. HTGQC and shinyHTGQC: an R package and shinyR application for quality controls of HTG EDGE-seq protocols. GigaByte 2022; 2022:gigabyte74. [PMID: 36950141 PMCID: PMC10027062 DOI: 10.46471/gigabyte.74] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/01/2022] [Indexed: 12/03/2022] Open
Abstract
Extraction-free HTG EdgeSeq protocols are used to profile sets of genes and measure their expression. Thus, these protocols are frequently used to characterise tumours and their microenvironments. However, although positive and control genes are provided, little indication is given concerning the assessment of the technical success of each sample within the sequencing run. We developed HTGQC, an R package for the quality control of HTG EdgeSeq protocols. Additionally, shinyHTGQC is a shiny application for users without computing knowledge, providing an easy-to-use interface for data quality control and visualisation. Quality checks can be performed on the raw sequencing outputs, and samples are flagged as FAIL or ALERT based on the expression levels of the positive and negative control genes. Availability & Implementation The code is freely available at https://github.com/LodovicoTerzi/HTGQC (R package) and https://lodovico.shinyapps.io/shinyHTGQC/ (shiny application), including test datasets.
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Affiliation(s)
- Lodovico Terzi di Bergamo
- Laboratory of Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland
- Bioinformatics Core Unit, Swiss Institute of Bioinformatics, Bellinzona, Switzerland
- Department of Health Science and Technology, Swiss Federal Institute of Technology (ETH Zürich), Zurich, Switzerland
- Corresponding author. E-mail:
| | - Francesca Guidetti
- Lymphoma Genomics unit, Institute of Oncology Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Davide Rossi
- Laboratory of Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland
| | - Francesco Bertoni
- Lymphoma Genomics unit, Institute of Oncology Research, Bellinzona, Switzerland
| | - Luciano Cascione
- Bioinformatics Core Unit, Swiss Institute of Bioinformatics, Bellinzona, Switzerland
- Lymphoma Genomics unit, Institute of Oncology Research, Bellinzona, Switzerland
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Tarantelli C, Cannas E, Ekeh H, Moscatello C, Gaudio E, Cascione L, Napoli S, Rech C, Testa A, Maniaci C, Rinaldi A, Zucca E, Stathis A, Ciulli A, Bertoni F. The bromodomain and extra-terminal domain degrader MZ1 exhibits preclinical anti-tumoral activity in diffuse large B-cell lymphoma of the activated B cell-like type. Explor Target Antitumor Ther 2021; 2:586-601. [PMID: 36046113 PMCID: PMC9400774 DOI: 10.37349/etat.2021.00065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 10/05/2021] [Accepted: 11/30/2021] [Indexed: 01/03/2023] Open
Abstract
Aim Bromodomain and extra-terminal domain (BET) proteins are epigenetic readers that play a fundamental role in transcription regulation. Preclinical and early clinical evidence sustain BET targeting as an anti-cancer approach. BET degraders are chimeric compounds comprising of a BET inhibitor, which allows the binding to BET bromodomains, linked to a small molecule, binder for an E3 ubiquitin ligase complex, triggering BET proteins degradation via the proteasome. These degraders, called proteolysis-targeting chimeras (PROTACs), can exhibit greater target specificity compared to BET inhibitors and overcome some of their limitations, such as the upregulation of the BET proteins themselves. Here are presented data on the anti-tumor activity and the mechanism of action of the BET degrader MZ1 in diffuse large B cell lymphoma (DLBCL) of the activated B-cell like (ABC, ABC DLBCL), using a BET inhibitor as a comparison. Methods Established lymphoma cell lines were exposed for 72 h to increasing doses of the compounds. Cell proliferation was evaluated by using an 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazoliumbromide (MTT) assay. Fluorescent-Activated Cell Sorter (FACS) analysis was performed to measure apoptotic activation and RNA sequencing (RNA-Seq) to study the transcriptional changes induced by the compounds. Results MZ1, and not its negative control epimer cisMZ1, was very active with a median half maximal inhibitory concentration (IC50) of 49 nmol/L. MZ1 was more in vitro active than the BET inhibitor birabresib (OTX015). Importantly, MZ1 induced cell death in all the ABC DLBCL cell lines, while the BET inhibitor was cytotoxic only in a fraction of them. BET degrader and inhibitor shared partially similar changes at transcriptome level but the MZ1 effect was stronger and overlapped with that caused cyclin-dependent kinase 9 (CDK9) inhibition. Conclusions The BET degrader MZ1 had strong cytotoxic activity in all the ABC DLBCL cell lines that were tested, and, at least in vitro, it elicited more profound effects than BET inhibitors, and encourages further investigations.
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Affiliation(s)
- Chiara Tarantelli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland
| | - Eleonora Cannas
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland
| | - Hillarie Ekeh
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland
| | - Carmelo Moscatello
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland
- Department of Medical, Oral and Biotechnological Sciences, “G. d’Annunzio” University of Chieti-Pescara, I-66100 Chieti, Italy
| | - Eugenio Gaudio
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland
- SIB Swiss Institute of Bioinformatics, 1000 Lausanne, Switzerland
| | - Sara Napoli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland
| | - Cesare Rech
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland
| | - Andrea Testa
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK
| | - Chiara Maniaci
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK
| | - Andrea Rinaldi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland
| | - Emanuele Zucca
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland
| | - Anastasios Stathis
- Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland
- Faculty of Biomedical Sciences, USI, 6900 Lugano, Switzerland
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland
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Milan L, Cascione L, Dalmasso F, Giovanella L, Chauvie S, Zucca E, Ceriani L. A validated PET radiomics model predicts outcome of diffuse large B cell lymphoma: post-hoc analysis from the SAKK38/07 clinical trial. Phys Med 2021. [DOI: 10.1016/s1120-1797(22)00197-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Sartori G, Napoli S, Cascione L, Chung EYL, Priebe V, Arribas AJ, Mensah AA, Dall'Angelo M, Falzarano C, Barnabei L, Forcato M, Rinaldi A, Bicciato S, Thome M, Bertoni F. ASB2 is a direct target of FLI1 that sustains NF-κB pathway activation in germinal center-derived diffuse large B-cell lymphoma. J Exp Clin Cancer Res 2021; 40:357. [PMID: 34763718 PMCID: PMC8582153 DOI: 10.1186/s13046-021-02159-3] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 10/28/2021] [Indexed: 12/13/2022]
Abstract
Background Diffuse large B-cell lymphoma (DLBCL) comprises at least two main biologically distinct entities: germinal center B-cell (GCB) and activated B-cell (ABC) subtype. Albeit sharing common lesions, GCB and ABC DLBCL present subtype-specific oncogenic pathway perturbations. ABC DLBCL is typically characterized by a constitutively active NF-kB. However, the latter is seen in also 30% of GCB DLBCL. Another recurrent lesion in DLBCL is an 11q24.3 gain, associated with the overexpression of two ETS transcription factors, ETS1 and FLI1. Here, we showed that FLI1 is more expressed in GCB than ABC DLBCL and we characterized its transcriptional network. Methods Gene expression data were obtained from public datasets GSE98588, phs001444.v2.p1, GSE95013 and GSE10846. ChIP-Seq for FLI1 paired with transcriptome analysis (RNA-Seq) after FLI1 silencing (siRNAs) was performed. Sequencing was carried out using the NextSeq 500 (Illumina). Detection of peaks was done using HOMER (v2.6); differential expressed genes were identified using moderated t-test (limma R-package) and functionally annotated with g:Profiler. ChIP-Seq and RNA-Seq data from GCB DLBCL cell lines after FLI1 downregulation were integrated to identify putative direct targets of FLI1. Results Analysis of clinical DLBCL specimens showed that FLI1 gene was more frequently expressed at higher levels in GCB than in ABC DLBCL and its protein levels were higher in GCB than in ABC DLBCL cell lines. Genes negatively regulated by FLI1 included tumor suppressor genes involved in negative regulation of cell cycle and hypoxia. Among positively regulated targets of FLI1, we found genes annotated for immune response, MYC targets, NF-κB and BCR signaling and NOTCH pathway genes. Of note, direct targets of FLI1 overlapped with genes regulated by ETS1, the other transcription factor gained at the 11q24.3 locus in DLBCL, suggesting a functional convergence within the ETS family. Positive targets of FLI1 included the NF-κB-associated ASB2, a putative essential gene for DLBCL cell survival. ASB2 gene downregulation was toxic in GCB DLBCL cell lines and induced NF-κB inhibition via downregulation of RelB and increased IκBα. Additionally, downregulation of FLI1, but not ASB2, caused reduction of NF-κB1 and RelA protein levels. Conclusions We conclude that FLI1 directly regulates a network of biologically crucial genes and processes in GCB DLBCL. FLI1 regulates both the classical NF-κB pathway at the transcriptional level, and the alternative NF-κB pathway, via ASB2. FLI1 and ASB2 inhibition represents a potential novel therapeutic approach for GCB DLBCL. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02159-3.
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Affiliation(s)
- Giulio Sartori
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, via Francesco Chiesa 5, 6500, Bellinzona, Switzerland
| | - Sara Napoli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, via Francesco Chiesa 5, 6500, Bellinzona, Switzerland
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, via Francesco Chiesa 5, 6500, Bellinzona, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Elaine Yee Lin Chung
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, via Francesco Chiesa 5, 6500, Bellinzona, Switzerland
| | - Valdemar Priebe
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, via Francesco Chiesa 5, 6500, Bellinzona, Switzerland
| | - Alberto Jesus Arribas
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, via Francesco Chiesa 5, 6500, Bellinzona, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Afua Adjeiwaa Mensah
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, via Francesco Chiesa 5, 6500, Bellinzona, Switzerland
| | - Michela Dall'Angelo
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, via Francesco Chiesa 5, 6500, Bellinzona, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Computer Science, University of Verona, Verona, Italy
| | - Chiara Falzarano
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, via Francesco Chiesa 5, 6500, Bellinzona, Switzerland
| | - Laura Barnabei
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, via Francesco Chiesa 5, 6500, Bellinzona, Switzerland
| | - Mattia Forcato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Andrea Rinaldi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, via Francesco Chiesa 5, 6500, Bellinzona, Switzerland
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Margot Thome
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, via Francesco Chiesa 5, 6500, Bellinzona, Switzerland. .,Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland.
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Frazzi R, Cusenza VY, Pistoni M, Canovi L, Cascione L, Bertoni F, Merli F. KLF4, DAPK1 and SPG20 promoter methylation is not affected by DNMT1 silencing and hypomethylating drugs in lymphoma cells. Oncol Rep 2021; 47:10. [PMID: 34751409 PMCID: PMC8600396 DOI: 10.3892/or.2021.8221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/11/2021] [Indexed: 11/05/2022] Open
Abstract
Promoter methylation represents one of the major epigenetic mechanisms responsible for the regulation of gene expression. Hypomethylating drugs are currently approved for the treatment of myelodysplastic syndromes and acute myeloid leukemia, and some studies have recently been carried out on diffuse large B cell lymphoma (DLBCL). DLBCL is a type of Non-Hodgkin lymphoma. The aim of the present study was to assess the role of DNA methyltransferase (DNMT)1 in mediating the epigenetic regulation of some key targets previously emerged as hypermethylated in Non-Hodgkin lymphoma. Reverse transcription-quantitative PCR, genome-wide arrays and methylation-specific PCR were used to determine the level of methylation of specific targets. Gene silencing, gene expression and immunoblotting were used to investigate the role of DNMT1 and DNMT3a in lymphoma cells. The present study showed that lymphoma cell lines displayed a completely different methylation profile on selected targets compared with primary B lymphocytes and peripheral blood mononuclear cells. 5′-aza-cytidine (5AZA) and 5′-aza-2-deoxycitidine (decitabine) exerted their activity through, at least in part, mechanisms independent of DNMT1 downregulation. Despite a global hypomethylating effect of 5AZA and decitabine, DNMT1 was not found to be necessary to maintain the hypermethylation of Krüppel-like factor 4 (KLF4), death associated protein 1 (DAPK1) and spastic paraplegia 20 (SPG20). SPG20 was found to be a completely methylated target in all the tested cell lines, but not in peripheral blood mononuclear cells, suggesting its association with malignancy. The highest methylation was clustered upstream of the transcription starting site in a panel of 28 DLBCL cell lines and the results were unaffected by the silencing of DNMT1 expression. These data demonstrated the epigenetic regulation of SPG20 in lymphoid cells and identified a number of novel markers associated with lymphomas that deserve further investigation.
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Affiliation(s)
- Raffaele Frazzi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale ‑ IRCCS di Reggio Emilia, I‑42123 Reggio Emilia, Emilia‑Romagna, Italy
| | - Vincenza Ylenia Cusenza
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale ‑ IRCCS di Reggio Emilia, I‑42123 Reggio Emilia, Emilia‑Romagna, Italy
| | - Mariaelena Pistoni
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale ‑ IRCCS di Reggio Emilia, I‑42123 Reggio Emilia, Emilia‑Romagna, Italy
| | - Laura Canovi
- Immunohematology and Transfusional Medicine Division, Azienda Unità Sanitaria Locale ‑ IRCCS di Reggio Emilia, I‑42123 Reggio Emilia, Emilia‑Romagna, Italy
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, University of Italian Switzerland, 6501 Bellinzona, Ticino, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, University of Italian Switzerland, 6501 Bellinzona, Ticino, Switzerland
| | - Francesco Merli
- Hematology Division, Azienda Unità Sanitaria Locale ‑ IRCCS di Reggio Emilia, I‑42123 Reggio Emilia, Emilia‑Romagna, Italy
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Ceriani L, Milan L, Cascione L, Gritti G, Dalmasso F, Esposito F, Pirosa MC, Schär S, Bruno A, Dirnhofer S, Giovanella L, Hayoz S, Mamot C, Rambaldi A, Chauvie S, Zucca E. Generation and validation of a PET radiomics model that predicts survival in diffuse large B cell lymphoma treated with R-CHOP14: A SAKK 38/07 trial post-hoc analysis. Hematol Oncol 2021; 40:11-21. [PMID: 34714558 DOI: 10.1002/hon.2935] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 12/24/2022]
Abstract
Functional parameters from positron emission tomography (PET) seem promising biomarkers in various lymphoma subtypes. This study investigated the prognostic value of PET radiomics in diffuse large B-cell lymphoma (DLBCL) patients treated with R-CHOP given either every 14 (testing set) or 21 days (validation set). Using the PyRadiomics Python package, 107 radiomics features were extracted from baseline PET scans of 133 patients enrolled in the Swiss Group for Clinical Cancer Research 38/07 prospective clinical trial (SAKK 38/07) [ClinicalTrial.gov identifier: NCT00544219]. The international prognostic indices, the main clinical parameters and standard PET metrics, together with 52 radiomics uncorrelated features (selected using the Spearman correlation test) were included in a least absolute shrinkage and selection operator (LASSO) Cox regression to assess their impact on progression-free (PFS), cause-specific (CSS), and overall survival (OS). A linear combination of the resulting parameters generated a prognostic radiomics score (RS) whose area under the curve (AUC) was calculated by receiver operating characteristic analysis. The RS efficacy was validated in an independent cohort of 107 DLBCL patients. LASSO Cox regression identified four radiomics features predicting PFS in SAKK 38/07. The derived RS showed a significant capability to foresee PFS in both testing (AUC, 0.709; p < 0.001) and validation (AUC, 0.706; p < 0.001) sets. RS was significantly associated also with CSS and OS in testing (CSS: AUC, 0.721; p < 0.001; OS: AUC, 0.740; p < 0.001) and validation (CSS: AUC, 0.763; p < 0.0001; OS: AUC, 0.703; p = 0.004) sets. The RS allowed risk classification of patients with significantly different PFS, CSS, and OS in both cohorts showing better predictive accuracy respect to clinical international indices. PET-derived radiomics may improve the prediction of outcome in DLBCL patients.
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Affiliation(s)
- Luca Ceriani
- Nuclear Medicine and PET/CT Centre, Imaging Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland.,Faculty of Biomedical Sciences, Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Lisa Milan
- Nuclear Medicine and PET/CT Centre, Imaging Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Luciano Cascione
- Faculty of Biomedical Sciences, Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Giuseppe Gritti
- Hematology Unit, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy
| | | | - Fabiana Esposito
- Medical Oncology, Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Maria Cristina Pirosa
- Medical Oncology, Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Sämi Schär
- Swiss Group for Clinical Cancer Research (SAKK) Coordinating Center, Bern, Switzerland
| | - Andrea Bruno
- Department of Nuclear Medicine, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy
| | - Stephan Dirnhofer
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Luca Giovanella
- Nuclear Medicine and PET/CT Centre, Imaging Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland.,Department of Nuclear Medicine, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Stefanie Hayoz
- Swiss Group for Clinical Cancer Research (SAKK) Coordinating Center, Bern, Switzerland
| | - Christoph Mamot
- Division of Oncology, Cantonal Hospital Aarau, Aarau, Switzerland
| | - Alessandro Rambaldi
- Hematology Unit, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Stephane Chauvie
- Medical Physics Unit, Santa Croce e Carlo Hospital, Cuneo, Italy
| | - Emanuele Zucca
- Faculty of Biomedical Sciences, Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland.,Medical Oncology, Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland.,Department of Medical Oncology, Bern University Hospital and University of Bern, Bern, Switzerland
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38
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Lampis A, Hahne JC, Gasparini P, Cascione L, Hedayat S, Vlachogiannis G, Murgia C, Fontana E, Edwards J, Horgan PG, Terracciano L, Sansom OJ, Martins CD, Kramer-Marek G, Croce CM, Braconi C, Fassan M, Valeri N. MIR21-induced loss of junctional adhesion molecule A promotes activation of oncogenic pathways, progression and metastasis in colorectal cancer. Cell Death Differ 2021; 28:2970-2982. [PMID: 34226680 PMCID: PMC8481293 DOI: 10.1038/s41418-021-00820-0] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 01/02/2023] Open
Abstract
Junctional adhesion molecules (JAMs) play a critical role in cell permeability, polarity and migration. JAM-A, a key protein of the JAM family, is altered in a number of conditions including cancer; however, consequences of JAM-A dysregulation on carcinogenesis appear to be tissue dependent and organ dependent with significant implications for the use of JAM-A as a biomarker or therapeutic target. Here, we test the expression and prognostic role of JAM-A downregulation in primary and metastatic colorectal cancer (CRC) (n = 947). We show that JAM-A downregulation is observed in ~60% of CRC and correlates with poor outcome in four cohorts of stages II and III CRC (n = 1098). Using JAM-A knockdown, re-expression and rescue experiments in cell line monolayers, 3D spheroids, patient-derived organoids and xenotransplants, we demonstrate that JAM-A silencing promotes proliferation and migration in 2D and 3D cell models and increases tumour volume and metastases in vivo. Using gene-expression and proteomic analyses, we show that JAM-A downregulation results in the activation of ERK, AKT and ROCK pathways and leads to decreased bone morphogenetic protein 7 expression. We identify MIR21 upregulation as the cause of JAM-A downregulation and show that JAM-A rescue mitigates the effects of MIR21 overexpression on cancer phenotype. Our results identify a novel molecular loop involving MIR21 dysregulation, JAM-A silencing and activation of multiple oncogenic pathways in promoting invasiveness and metastasis in CRC.
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Affiliation(s)
- Andrea Lampis
- Division of Molecular Pathology, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Jens C Hahne
- Division of Molecular Pathology, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Pierluigi Gasparini
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH, USA
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Luciano Cascione
- Bioinformatics Core Unit, Institute of Oncology Research (IOR), Faculty of Biomedical Sciences, Università della Svizzera italiana, Bellinzona, Switzerland
- Swiss Institute of Bioinformatics, Bellinzona, Switzerland
| | - Somaieh Hedayat
- Division of Molecular Pathology, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Georgios Vlachogiannis
- Division of Molecular Pathology, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | | | - Elisa Fontana
- Division of Molecular Pathology, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Joanne Edwards
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Paul G Horgan
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Luigi Terracciano
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- IRCCS Humanitas Research Hospital, Milan, Italy
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Carlos D Martins
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | | | - Carlo M Croce
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Chiara Braconi
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Matteo Fassan
- IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Medicine, Surgical Pathology Unit, University of Padua, Padua, Italy
- Istituto Oncologico Veneto, Istituto di Ricovero e Cura a Carattere Scientifico, Padua, Italy
| | - Nicola Valeri
- Division of Molecular Pathology, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Department of Medicine, The Royal Marsden Hospital, London, UK.
- Division of Surgery and Cancer, Imperial College London, London, UK.
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Arribas A, Napoli S, Cascione L, Sartori G, Gaudio E, Tarantelli C, Mensah A, Spriano F, Zucchetto A, Rossi F, Rinaldi A, Jovic S, Stathis A, Stussi G, Gattei V, Brown J, Esteller M, Zucca E, Rossi D, Bertoni F. 842P Secreted factors determine resistance to idelalisib in splenic marginal zone lymphoma (MZL) models. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Casadei L, Sarchet P, Cascione L, Nigita G, de Faria FCC, Croce CM, Grignol V, Pollock RE. Abstract 474: Extracellular vesicle - MDM2 as liquid biopsy biomarker for disease identification in retroperitoneal liposarcoma. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-474] [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: Extracellular vesicles (EVs) are membrane vesicles containing proteins and nucleic acids that aresecreted by all cells and circulate in the blood. In the tumor microenvironment their contents havebeen shown to carry important pro-carcinogenic molecules. Soft tissue sarcoma of theretroperitoneum of which the most common types are well differentiated/dedifferentiatedliposarcoma (WD/DDLPS) are marked by recurrence rates of >50% even after complete resection.A molecular hallmark of RLS WD/DDLPS are high levels of MDM2 DNA, a finding observed innearly all WD/DDLPS tumors. Indeed, FISH assessment of MDM2 in resected tissues is currentlythe definitive diagnostic methodology for WD/DDLPS. Prognosis in WD/DDLPS is enhanced byearly detection of recurrent lesions. However, current scanning technologies cannot resolverecurrent liposarcoma vs postoperative scarring in many patients (97% sensitivity/51%specificity); the need for easily retrieved and analyzed circulating factors that are diagnostic andprognostic is urgent.
Methods: A cohort of 11 WD/DDLPS serum samples were collected at the time of surgery and during followup visits (6-12 months after surgery). Serum from normal healthy people (N=15) were used as acontrol. EVs were isolated from the serum through precipitation technology (ExoQuick) andultracentrifugation. The EVs-DNA was then isolated and the level of MDM2 was measured by Q-PCR. The level of MDM2 DNA in the WD/DDLPS tissues was also measured by Q-PCR andcompared with Normal Adjacent tissues.
Results: MDM2 DNA was detected in EVs of the serum of RLS WD/DDLPS patients at significantly higherlevels than normal controls (geometric mean MDM2 DNA number of molecules value=74,434 vs10,146, p=0.0025). This increase was concordant with the level of MDM2 DNA as measured inWD/DDLPS tissues compared to normal adjacent tissues (p= 0.0009). Moreover, serumWD/DDLPS EV MDM2 was dramatically decreased in RLS WD/DDLPS patients after tumorresection (geometric mean MDM2 DNA number of molecules value pre-op=74,434 vs post-op=13,879, p=0.0048), and appears to correlate with CT-scan evidence of recurrent or persistentdisease after surgery. Importantly, the level of MDM2 DNA in EV's post-operatively decreasedreaching a level similar to the level of MDM2 in the controls (difference between post- surgeryand controls: p=0.47).
Conclusion: In conclusion RLS WD/DDLPS EVMDM2 may potentially serve as an efficacious RLSWD/DDLPS first-ever prognostic and therapy predictive biomarker for a lethal disease currentlylacking such determinants.
Citation Format: Lucia Casadei, Patricia Sarchet, Luciano Cascione, Giovanni Nigita, Fernanda Costas Casal de Faria, Carlo Maria Croce, Valerie Grignol, Raphael E. Pollock. Extracellular vesicle - MDM2 as liquid biopsy biomarker for disease identification in retroperitoneal liposarcoma [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 474.
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Affiliation(s)
| | | | - Luciano Cascione
- 2Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), iana, Bellinzona, Switzerland
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Hahne JC, Lampis A, Ghidini M, Ratti M, Senti C, Passalacqua R, Cascione L, Braconi C, Sansom O, Fassan M, Valeri N. Abstract 2373: Expression of exosomal let-7g in biofluids and outcome in colon cancer patient treated with anti-EGFR therapy. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2373] [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: Monoclonal antibodies against the Epidermal Growth Factor Receptor (EGFR) such as cetuximab or panitumumab are used for the treatment of metastatic colorectal cancer (mCRC) patients. Unfortunately, most patients develop resistance against these therapies within months. Several studies have shown that aberrations in the RAS pathway are responsible for resistance. However, even in metastases that are refractory to anti-EGFR treatment a significant fraction of RAS wild-type (wt) cells remain. These findings suggest a cross-talk between RAS mutant and wt cells in mediating resistance in the wt compartment.
Methods: Mouse and patient-derived organoids from mCRC as well as CRC cell lines were used to test the contribution of extracellular vesicles in mediating resistance in RAS wt cells. Using conditioned media, transfection experiments and liquid biopsies (plasma and urine) from patients differential expression of the let-7g microRNA was demonstrated in microvesicles from cetuximab sensitive and resistant cells. Changes in expression of let-7g were further analyzed by in-situ hybridization in tissues.
Results: Conditioned media from RAS mutant organoids rendered RAS wt organoids resistant against cetuximab treatment. Basal let-7g expression from pre-treatment plasma and urine samples of RAS wt patients correlated with clinical outcome and changes in let-7g circulating levels mirrored clinical behavior. In-situ hybridization in tissues confirmed changes in expression of the let-7g microRNA observed in plasma and urine samples.
Conclusions: Our data suggest that let-7g microRNA might function as a paracrine mediator of anti-EGFR resistance and might be exploited as a non-invasive biomarker of resistance to cetuximab treatment. Further work is ongoing to characterize the molecular mechanisms underpinning let-7g mediated effect on anti-EGFR sensitivity in RAS wt CRC cells.
Citation Format: Jens C. Hahne, Andrea Lampis, Michele Ghidini, Margherita Ratti, Chiara Senti, Rodolfo Passalacqua, Luciano Cascione, Chiara Braconi, Owen Sansom, Matteo Fassan, Nicola Valeri. Expression of exosomal let-7g in biofluids and outcome in colon cancer patient treated with anti-EGFR therapy [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 2373.
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Affiliation(s)
- Jens C. Hahne
- 1The Institute of Cancer Research, Sutton, United Kingdom
| | - Andrea Lampis
- 1The Institute of Cancer Research, Sutton, United Kingdom
| | - Michele Ghidini
- 2Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Chiara Senti
- 3ASST di Cremona, Ospedale di Cremona, Cremona, Italy
| | | | | | | | - Owen Sansom
- 6The Beatson Institute for Cancer Research, Glasgow, United Kingdom
| | | | - Nicola Valeri
- 1The Institute of Cancer Research, Sutton, United Kingdom
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Napoli S, Cascione L, Rinaldi A, Spriano F, Guidetti F, Zhang F, Cacciapuoti MT, Mensah AA, Sartori G, Munz N, Forcato M, Bicciato S, Chiappella A, Ghione P, Elemento O, Cerchietti L, Inghirami G, Bertoni F. Characterization of GECPAR, a noncoding RNA that regulates the transcriptional program of diffuse large B-cell lymphoma. Haematologica 2021; 107:1131-1143. [PMID: 34162177 PMCID: PMC9052922 DOI: 10.3324/haematol.2020.267096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Indexed: 01/09/2023] Open
Abstract
Enhancers are regulatory regions of DNA, which play a key role in cell-type specific differentiation and development. Most active enhancers are transcribed into enhancer RNA (eRNA) that can regulate transcription of target genes by means of in cis as well as in trans action. eRNA stabilize contacts between distal genomic regions and mediate the interaction of DNA with master transcription factors. Here, we characterized an enhancer eRNA, GECPAR (germinal center proliferative adapter RNA), which is specifically transcribed in normal and neoplastic germinal center B cells from the super-enhancer of POU2AF1, a key regulatory gene of the germinal center reaction. Using diffuse large B-cell lymphoma cell line models, we demonstrated the tumor suppressor activity of GECPAR, which is mediated via its transcriptional regulation of proliferation and differentiation genes, particularly MYC and the Wnt pathway.
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Affiliation(s)
- Sara Napoli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,SARA NAPOLI
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Andrea Rinaldi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Filippo Spriano
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Francesca Guidetti
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Fangwen Zhang
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | | | - Afua Adjeiwaa Mensah
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Giulio Sartori
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Nicolas Munz
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Mattia Forcato
- Center for Genome Research, Department of Life Sciences University of Modena and Reggio, Modena, Italy
| | - Silvio Bicciato
- Center for Genome Research, Department of Life Sciences University of Modena and Reggio, Modena, Italy
| | - Annalisa Chiappella
- Ematologia, A.O.U. Città della Salute e della Scienza di Torino, Turin, Italy
| | - Paola Ghione
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Leandro Cerchietti
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Giorgio Inghirami
- Pathology and Laboratory Medicine Department, Weill Cornell Medicine, New York, NY, USA
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,Oncology Institute of Southern Switzerland, Bellinzona, Switzerland,FRANCESCO BERTONI
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Genta S, Ghilardi G, Cascione L, Juskevicius D, Tzankov A, Schär S, Giovanella L, Hayoz S, Mamot C, Dirnhofer S, Zucca E, Ceriani L. INTEGRATION OF BASELINE METABOLIC PARAMETERS AND MUTATIONAL PROFILE PREDICTS OUTCOME IN DLBCL PATIENTS. A
POST HOC
ANALYSIS OF SAKK38/07 STUDY. Hematol Oncol 2021. [DOI: 10.1002/hon.18_2879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- S Genta
- Oncology Institute of Southern Switzerland Clinic of Medical Oncology Bellinzona Switzerland
| | - G Ghilardi
- Oncology Institute of Southern Switzerland Clinic of Hematology Bellinzona Switzerland
| | - L Cascione
- Università della Svizzera Italiana Institute of Oncology Research Faculty of Biomedical Sciences Bellinzona Switzerland
| | - D Juskevicius
- University Hospital Basel, University of Basel Institute of Medical Genetics and Pathology Basel Switzerland
| | - A Tzankov
- University Hospital Basel, University of Basel Institute of Medical Genetics and Pathology Basel Switzerland
| | - S Schär
- Swiss Group for Clinical Cancer Research (SAKK) Coordinating Center Coordinating Center Bern Switzerland
| | - L Giovanella
- Imaging Institute of Southern Switzerland Ente Ospedaliero Cantonale Clinic of Nuclear Medicine and PET/CT Center Bellinzona Switzerland
| | - S Hayoz
- Swiss Group for Clinical Cancer Research (SAKK) Coordinating Center Coordinating Center Bern Switzerland
| | - C Mamot
- Cantonal Hospital Aarau Division of Oncology Aarau Switzerland
| | - S Dirnhofer
- University Hospital Basel, University of Basel Institute of Medical Genetics and Pathology Basel Switzerland
| | - E Zucca
- Oncology Institute of Southern Switzerland Clinic of Medical Oncology Bellinzona Switzerland
| | - L Ceriani
- Imaging Institute of Southern Switzerland Ente Ospedaliero Cantonale Clinic of Nuclear Medicine and PET/CT Center Bellinzona Switzerland
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La Ferlita A, Alaimo S, Di Bella S, Martorana E, Laliotis GI, Bertoni F, Cascione L, Tsichlis PN, Ferro A, Bosotti R, Pulvirenti A. RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis. BMC Bioinformatics 2021; 22:298. [PMID: 34082707 PMCID: PMC8173825 DOI: 10.1186/s12859-021-04211-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 11/08/2020] [Accepted: 05/20/2021] [Indexed: 12/13/2022] Open
Abstract
Background RNA-Seq is a well-established technology extensively used for transcriptome profiling, allowing the analysis of coding and non-coding RNA molecules. However, this technology produces a vast amount of data requiring sophisticated computational approaches for their analysis than other traditional technologies such as Real-Time PCR or microarrays, strongly discouraging non-expert users. For this reason, dozens of pipelines have been deployed for the analysis of RNA-Seq data. Although interesting, these present several limitations and their usage require a technical background, which may be uncommon in small research laboratories. Therefore, the application of these technologies in such contexts is still limited and causes a clear bottleneck in knowledge advancement. Results Motivated by these considerations, we have developed RNAdetector, a new free cross-platform and user-friendly RNA-Seq data analysis software that can be used locally or in cloud environments through an easy-to-use Graphical User Interface allowing the analysis of coding and non-coding RNAs from RNA-Seq datasets of any sequenced biological species. Conclusions RNAdetector is a new software that fills an essential gap between the needs of biomedical and research labs to process RNA-Seq data and their common lack of technical background in performing such analysis, which usually relies on outsourcing such steps to third party bioinformatics facilities or using expensive commercial software. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04211-7.
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Affiliation(s)
- Alessandro La Ferlita
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy.,Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA.,Department of Physics and Astronomy, University of Catania, Catania, Italy
| | - Salvatore Alaimo
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy
| | | | - Emanuele Martorana
- Regional Referral Centre for Rare Lung Diseases, A. O. U. "Policlinico-Vittorio Emanuele", Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Georgios I Laliotis
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | | | | | - Philip N Tsichlis
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy
| | | | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy.
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45
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Bonfiglio F, Bruscaggin A, Guidetti F, Terzi di Bergamo L, Faderl M, Spina V, Condoluci A, Bonomini L, Forestieri G, Koch R, Piffaretti D, Pini K, Pirosa MC, Cittone MG, Arribas A, Lucioni M, Ghilardi G, Wu W, Arcaini L, Baptista MJ, Bastidas G, Bea S, Boldorini R, Broccoli A, Canzonieri V, Cascione L, Ceriani L, Cogliatti S, Derenzini E, Devizzi L, Dietrich S, Elia AR, Facchetti F, Gaidano G, Garcia JF, Gerber B, Ghia P, Silva MG, Gritti G, Guidetti A, Hitz F, Inghirami G, Ladetto M, Lopez‐Guillermo A, Lucchini E, Maiorana A, Marasca R, Matutes E, Meignin V, Merli M, Moccia A, Mollejo M, Montalban C, Novak U, Oscier DG, Passamonti F, Piazza F, Pizzolitto S, Sabattini E, Salles G, Santambrogio E, Scarfó L, Stathis A, Stüssi G, Geyer JT, Tapia G, Thieblemont C, Tousseyn T, Tucci A, Visco C, Vitolo U, Zenz T, Zinzani PL, Khiabanian H, Calcinotto A, Bertoni F, Bhagat G, Campo E, Leval L, Dirnhofer S, Pileri SA, Piris MÁ, Traverse‐Glehen A, Tzankov A, Paulli M, Ponzoni M, Mazzucchelli L, Cavalli F, Zucca E, Rossi D. GENETIC AND PHENOTYPIC ATTRIBUTES OF SPLENIC MARGINAL ZONE LYMPHOMA. Hematol Oncol 2021. [DOI: 10.1002/hon.43_2879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Ferrero S, Moia R, Cascione L, Zaccaria GM, Rinaldi A, Alessandria B, Grimaldi D, Favini C, Evangelista A, Schipani M, Narni F, Stelitano C, Stefani PM, Benedetti F, Mian M, Casaroli I, Zanni M, Castellino C, Pavone V, Galimberti S, Re F, Rossi D, Cortelazzo S, Gaidano G, Ladetto M, Bertoni F. A COMPLETELY GENETIC PROGNOSTIC MODEL OVERCOMES CLINICAL PROGNOSTICATORS IN MANTLE CELL LYMPHOMA: RESULTS FROM THE MCL0208 TRIAL FROM THE FONDAZIONE ITALIANA LINFOMI (FIL). Hematol Oncol 2021. [DOI: 10.1002/hon.59_2879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- S. Ferrero
- Hematology Department of Molecular Biotechnologies and Health Sciences University of Torino Hematology 1, AOU "Città della salute e della scienza di Torino" Torino Italy
| | - R. Moia
- Division of Hematology Department of Translational Medicine Università del Piemonte Orientale Novara Italy
| | - L. Cascione
- Institute of Oncology Research Faculty of Biomedical Sciences USI, Bellinzona SIB Swiss Institute of Bioinformatics Lausanne Switzerland
| | - G. M. Zaccaria
- Hematology and Cell Therapy Unit IRCCS Istituto Tumori 'Giovanni Paolo II' Bari Italy
| | - A. Rinaldi
- Institute of Oncology Research Faculty of Biomedical Sciences USI Bellinzona Switzerland
| | - B. Alessandria
- Hematology Department of Molecular Biotechnologies and Health Sciences University of Torino Torino Italy
| | - D. Grimaldi
- Hematology Department of Molecular Biotechnologies and Health Sciences University of Torino Torino Italy
| | - C. Favini
- Division of Hematology Department of Translational Medicine Università del Piemonte Orientale Novara Italy
| | - A. Evangelista
- Unit of Cancer Epidemiology CPO Piemonte A.O.U. Città della Salute e della Scienza di Torino Torino Italy
| | - M. Schipani
- Division of Hematology Department of Translational Medicine Università del Piemonte Orientale Novara Italy
| | - F. Narni
- Department of Medical and Surgical Sciences Section of Hematology University of Modena and Reggio Emilia Azienda Ospedaliero Universitaria Policlinico Modena Italy
| | - C. Stelitano
- Hematology Department AO "Bianchi‐Melacrino‐Morelli" Reggio Calabria Italy
| | - P. M. Stefani
- Hematology Unit General Hospital Ca' Foncello Treviso Italy
| | - F. Benedetti
- Hematology University Division Verona Hospital Verona Italy
| | - M. Mian
- Department of Haematology and CBMT Bolzano Hospital Bolzano Italy
| | - I. Casaroli
- Haematology Unit ASST Monza San Gerardo Monza Italy
| | - M. Zanni
- Hematology Unit Azienda Ospedaliera SS Antonio e Biagio e Cesare Arrigo Alessandria Italy
| | - C. Castellino
- Department of Hematology S. Croce e Carle Hospital Cuneo Italy
| | - V. Pavone
- UOC Ematologia e Trapianto Az. Osp. C. Panico Tricase Italy
| | - S. Galimberti
- Section of Hematology Department of Clinical and Experimental Medicine University of Pisa Pisa Italy
| | - F. Re
- Haematology and Bone Marrow Transplant Unit Parma General Hospital Parma Italy
| | - D. Rossi
- Institute of Oncology Research Faculty of Biomedical Sciences USI, Bellinzona, Switzerland Oncology Institute of Southern Switzerland (IOSI) Bellinzona,Bellinzona Switzerland
| | - S. Cortelazzo
- Oncology Unit Italy Medical & Center Hospital Humanitas Gavazzeni and Castelli Bergamo Italy
| | - G. Gaidano
- Division of Hematology Department of Translational Medicine Università del Piemonte Orientale Novara Italy
| | - M. Ladetto
- Division of Hematology Department of Translational Medicine Università del Piemonte Orientale Novara, Division of Hematology Azienda Ospedaliera SS Antonio e Biagio e Cesare Arrigo Alessandria Italy
| | - F. Bertoni
- Institute of Oncology Research Faculty of Biomedical Sciences USI, Bellinzona, Switzerland Oncology Institute of Southern Switzerland (IOSI) Bellinzona,Bellinzona Switzerland
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Ceriani L, Milan L, Cascione L, Gritti G, Dalmasso F, Esposito F, Schär S, Bruno A, Dirnhofer S, Giovanella L, Hayoz S, Mamot C, Rambaldi A, Chauvie S, Zucca E. DEVELOPMENT AND VALIDATION OF A PET RADIOMICS PROGNOSTIC MODEL FOR DIFFUSE LARGE B CELL LYMPHOMA. Hematol Oncol 2021. [DOI: 10.1002/hon.22_2879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- L Ceriani
- Ente Ospedaliero Cantonale Clinic of Nuclear Medicine and PET/CT Center Lugano Switzerland
| | - L Milan
- Ente Ospedaliero Cantonale Clinic of Nuclear Medicine and PET/CT Center Lugano Switzerland
| | - L Cascione
- Università della Svizzera Italiana Institute of Oncology Research Faculty of Biomedical Sciences Bellinzona Switzerland
| | - G Gritti
- Azienda Ospedaliera Papa Giovanni XXIII Hematology Unit Bergamo Italy
| | - F Dalmasso
- Santa Croce e Carle Hospital Medical Physics Unit Cuneo Italy
| | - F Esposito
- Ente Ospedaliero Cantonale Institute of Southern Switzerland Clinic of Medical Oncology Bellinzona Switzerland
| | - Säm Schär
- Swiss Group for Clinical Cancer Research (SAKK) Swiss Group for Clinical Cancer Research (SAKK) Coordinating Center Bern Switzerland
| | - A Bruno
- Azienda Ospedaliera Papa Giovanni XXIII Department of Nuclear Medicine Bergamo Italy
| | - S Dirnhofer
- University Hospital Basel Institute of Medical Genetics and Pathology Basel Switzerland
| | - L Giovanella
- Ente Ospedaliero Cantonale Clinic of Nuclear Medicine and PET/CT Center Lugano Switzerland
| | - S Hayoz
- Swiss Group for Clinical Cancer Research (SAKK) Swiss Group for Clinical Cancer Research (SAKK) Coordinating Center Bern Switzerland
| | - C Mamot
- Cantonal Hospital Aarau Division of Oncology Aarau Switzerland
| | - A Rambaldi
- Azienda Ospedaliera Papa Giovanni XXIII Hematology Unit Bergamo Italy
| | - S Chauvie
- Santa Croce e Carle Hospital Medical Physics Unit Cuneo Italy
| | - E Zucca
- Ente Ospedaliero Cantonale Institute of Southern Switzerland Clinic of Medical Oncology Bellinzona Switzerland
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Munz N, Cascione L, Parmigiani L, Tarantelli C, Rinaldi A, Cmiljanovic N, Cmiljanovic V, Giugno R, Bertoni F, Napoli S. Exon-Intron Differential Analysis Reveals the Role of Competing Endogenous RNAs in Post-Transcriptional Regulation of Translation. Noncoding RNA 2021; 7:ncrna7020026. [PMID: 33923420 PMCID: PMC8167571 DOI: 10.3390/ncrna7020026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/07/2021] [Accepted: 04/14/2021] [Indexed: 12/15/2022] Open
Abstract
Stressful conditions induce the cell to save energy and activate a rescue program modulated by mammalian target of rapamycin (mTOR). Along with transcriptional and translational regulation, the cell relies also on post-transcriptional modulation to quickly adapt the translation of essential proteins. MicroRNAs play an important role in the regulation of protein translation, and their availability is tightly regulated by RNA competing mechanisms often mediated by long noncoding RNAs (lncRNAs). In our paper, we simulated the response to growth adverse condition by bimiralisib, a dual PI3K/mTOR inhibitor, in diffuse large B cell lymphoma cell lines, and we studied post-transcriptional regulation by the differential analysis of exonic and intronic RNA expression. In particular, we observed the upregulation of a lncRNA, lncTNK2-2:1, which correlated with the stabilization of transcripts involved in the regulation of translation and DNA damage after bimiralisib treatment. We identified miR-21-3p as miRNA likely sponged by lncTNK2-2:1, with consequent stabilization of the mRNA of p53, which is a master regulator of cell growth in response to DNA damage.
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Affiliation(s)
- Nicolas Munz
- Institute of Oncology Research, Faculty of Biomedical Sciences, Universita`Svizzera Italiana, 6500 Bellinzona, Switzerland; (N.M.); (L.C.); (C.T.); (A.R.); (F.B.)
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, Universita`Svizzera Italiana, 6500 Bellinzona, Switzerland; (N.M.); (L.C.); (C.T.); (A.R.); (F.B.)
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Luca Parmigiani
- Computer Science Department, University of Verona, 37129 Verona, Italy; (L.P.); (R.G.)
| | - Chiara Tarantelli
- Institute of Oncology Research, Faculty of Biomedical Sciences, Universita`Svizzera Italiana, 6500 Bellinzona, Switzerland; (N.M.); (L.C.); (C.T.); (A.R.); (F.B.)
| | - Andrea Rinaldi
- Institute of Oncology Research, Faculty of Biomedical Sciences, Universita`Svizzera Italiana, 6500 Bellinzona, Switzerland; (N.M.); (L.C.); (C.T.); (A.R.); (F.B.)
| | | | | | - Rosalba Giugno
- Computer Science Department, University of Verona, 37129 Verona, Italy; (L.P.); (R.G.)
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, Universita`Svizzera Italiana, 6500 Bellinzona, Switzerland; (N.M.); (L.C.); (C.T.); (A.R.); (F.B.)
- Oncology Institute of Southern Switzerland, 6500 Bellinzona, Switzerland
| | - Sara Napoli
- Institute of Oncology Research, Faculty of Biomedical Sciences, Universita`Svizzera Italiana, 6500 Bellinzona, Switzerland; (N.M.); (L.C.); (C.T.); (A.R.); (F.B.)
- Correspondence:
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49
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Ceriani L, Milan L, Virili C, Cascione L, Paone G, Trimboli P, Giovanella L. Radiomics Analysis of [ 18F]-Fluorodeoxyglucose-Avid Thyroid Incidentalomas Improves Risk Stratification and Selection for Clinical Assessment. Thyroid 2021; 31:88-95. [PMID: 32517585 DOI: 10.1089/thy.2020.0224] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background: [18F]-Fluorodeoxyglucose (FDG)-avid thyroid lesions incidentally detected on positron emission tomography/computed tomography (PET/CT) scans represent a tumor lesion in about 30% of cases. The present study evaluated the ability of PET metrics and radiomics features to predict final diagnosis of [18F]FDG thyroid incidentalomas (TIs). Methods: A total of 104 patients with 107 TIs were retrospectively studied; 30 nodules (28%) were diagnosed as malignant. After volumetric segmentation of each thyroid lesion, metabolic tumor volume (MTV), total lesion glycolysis (TLG), standardized uptake values (SUVs), and metabolic heterogeneity were estimated, and 107 radiomics features were extracted following a standard protocol. Results: MTV, TLG, SUVmax, SUVmean, and SUVpeak among functional PET parameters, and gray-level co-occurrence matrix (GLCM)_InverseDifferenceMoment, shape_Sphericity, GLCM_SumSquares, firstorder_Maximum2DDiameterSlice, firstorder_Energy, and GLCM_Contrast among nonredundant radiomics features, showed significantly different values between malignant and benign TIs (Mann-Whitney U-test, p < 0.01 for all). Univariate logistic regression revealed that these parameters demonstrated good ability to predict final diagnosis of TIs (p < 0.02 for all). Shape_Sphericity was the best predictor classifying 82% of TIs correctly (p < 0.0001). Only TLG, SUVmax, and shape_Sphericity retained significance (p < 0.0001) by multivariate analysis. Malignant lesion prevalence increased from 7% to 100% in accordance with the number (score, 0-3) of the three positive parameters present (χ2 trend, p < 0.0001). A score of 0 excludes malignant TIs with a negative predictive value of 93%, while a score of 3 predicted malignancy with a positive predictive value of 100%. Conclusions: PET metrics and radiomics analysis can improve identification of [18F]FDG-avid TIs at high risk of malignancy. A model based on TLG, SUVmax, and shape_Sphericity may allow prediction of a final diagnosis, providing useful information for the management of TIs.
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Affiliation(s)
- Luca Ceriani
- Clinic for Nuclear Medicine and Molecular Imaging, Imaging Institute of Southern Switzerland, Lugano, Switzerland
- Institute of Oncology Research, Faculty of Biomedical Sciences, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Lisa Milan
- Clinic for Nuclear Medicine and Molecular Imaging, Imaging Institute of Southern Switzerland, Lugano, Switzerland
| | - Camilla Virili
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, Università della Svizzera italiana, Bellinzona, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Amphipole, Lausanne, Switzerland
| | - Gaetano Paone
- Clinic for Nuclear Medicine and Molecular Imaging, Imaging Institute of Southern Switzerland, Lugano, Switzerland
| | - Pierpaolo Trimboli
- Clinic for Nuclear Medicine and Molecular Imaging, Imaging Institute of Southern Switzerland, Lugano, Switzerland
- Competence Centre for Thyroid Diseases, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Lugano, Switzerland
| | - Luca Giovanella
- Clinic for Nuclear Medicine and Molecular Imaging, Imaging Institute of Southern Switzerland, Lugano, Switzerland
- Competence Centre for Thyroid Diseases, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Clinic for Nuclear Medicine, University Hospital and University of Zurich, Zurich, Switzerland
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50
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Abstract
Copy number aberrations (CNV/CNA) represent a major contribution to the somatic mutation landscapes in cancers, and their identification can lead to the discovery of oncogenetic targets as well as improved disease (sub-) classification. Diffuse large B cell lymphoma (DLBCL) is the most common lymphoma in Western Countries and up to 40% of the affected individuals still succumb to the disease. DLBCL is an heterogenous group of disorders, and we call DLBCL today is not necessarily the same disease of a few years ago. This review focuses on types and frequencies of regional DNA CNVs in DLBCL, not otherwise specified, and in two particular conditions, the transformation from indolent lymphomas and the DLBCL in individuals with immunodeficiency.
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Affiliation(s)
- Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Luca Aresu
- Department of Veterinary Science, University of Turin, Grugliasco, Italy
| | - Michael Baudis
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Molecular Life Science, University of Zurich, Zurich, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland.,Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
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