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Syrykh C, Pons-Brun B, Russiñol N, Playa-Albinyana H, Baumann T, Duran-Ferrer M, Kulis M, Carbó-Meix A, Mozas P, Alcoceba M, González M, Navarro-Bailón A, Colado E, Payer ÁR, Aymerich M, Terol MJ, Lu J, Knisbacher BA, Hahn CK, Ruiz-Gaspà S, Enjuanes A, Wu CJ, Getz G, Zenz T, López-Guillermo A, Martín-Subero JI, Colomer D, Delgado J, Campo E, Nadeu F. IGLV3-21R110 mutation has prognostic value in patients with treatment-naive chronic lymphocytic leukemia. Blood Adv 2023; 7:7384-7391. [PMID: 37505099 PMCID: PMC10726246 DOI: 10.1182/bloodadvances.2023010132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/29/2023] Open
Affiliation(s)
- Charlotte Syrykh
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Department of Pathology, Institut Universitaire du Cancer, CHU de Toulouse, Toulouse, France
| | - Berta Pons-Brun
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Núria Russiñol
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Heribert Playa-Albinyana
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | | | - Martí Duran-Ferrer
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Marta Kulis
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Anna Carbó-Meix
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Pablo Mozas
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Hospital Clínic of Barcelona, Barcelona, Spain
| | - Miguel Alcoceba
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Biología Molecular e Histocompatibilidad, Instituto de Investigación Biomédica de Salamanca-Hospital Universitario, Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer, University of Salamanca-Spanish National Research Council, Salamanca, Spain
| | - Marcos González
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Biología Molecular e Histocompatibilidad, Instituto de Investigación Biomédica de Salamanca-Hospital Universitario, Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer, University of Salamanca-Spanish National Research Council, Salamanca, Spain
| | - Almudena Navarro-Bailón
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Biología Molecular e Histocompatibilidad, Instituto de Investigación Biomédica de Salamanca-Hospital Universitario, Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer, University of Salamanca-Spanish National Research Council, Salamanca, Spain
| | - Enrique Colado
- Servicio de Hematología y Hemoterapia, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Ángel R. Payer
- Servicio de Hematología y Hemoterapia, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Marta Aymerich
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Hospital Clínic of Barcelona, Barcelona, Spain
| | - María J. Terol
- Servicio de Hematología, Hospital Clínico Universitario, Instituto de Investigación Sanitaria (INCLIVA), Universidad de Valencia, Valencia, Spain
| | - Junyan Lu
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Binyamin A. Knisbacher
- The Broad Institute of MIT and Harvard, Cambridge, MA
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Cynthia K. Hahn
- The Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Sílvia Ruiz-Gaspà
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Anna Enjuanes
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Catherine J. Wu
- The Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Thorsten Zenz
- Department of Medical Oncology and Hematology, University Hospital and University of Zürich, Zurich, Switzerland
| | - Armando López-Guillermo
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Hospital Clínic of Barcelona, Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - José I. Martín-Subero
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Universitat de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Dolors Colomer
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Hospital Clínic of Barcelona, Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - Julio Delgado
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Hospital Clínic of Barcelona, Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - Elías Campo
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Hospital Clínic of Barcelona, Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - Ferran Nadeu
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
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2
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Martín García-Sancho A, Baile M, Rodríguez G, Dlouhy I, Sancho JM, Jarque I, González-Barca E, Salar A, Espeso M, Grande C, Bergua J, Montes-Moreno S, Redondo A, Enjuanes A, Campo E, López-Guillermo A, Caballero D. Lenalidomide in combination with R-ESHAP in patients with relapsed or refractory diffuse large B-cell lymphoma: A phase 2 study from GELTAMO. Br J Haematol 2023; 203:202-211. [PMID: 37485564 DOI: 10.1111/bjh.18989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/18/2023] [Accepted: 07/10/2023] [Indexed: 07/25/2023]
Abstract
Diffuse large B-cell lymphoma (DLBCL) patients with relapsed or refractory (RR) disease have poor outcomes with current salvage regimens. We conducted a phase 2 trial to analyse the safety and efficacy of adding lenalidomide to R-ESHAP (LR-ESHAP) in patients with RR DLBCL. Subjects received 3 cycles of lenalidomide 10 mg/day on days 1-14 of every 21-day cycle, in combination with R-ESHAP at standard doses. Responding patients underwent autologous stem-cell transplantation (ASCT). The primary endpoint was the overall response rate (ORR) after 3 cycles. Centralized cell-of-origin (COO) classification was performed. Forty-six patients were included. The ORR after LR-ESHAP was 67% (35% of patients achieved complete remission). Patients with primary refractory disease (n = 26) had significantly worse ORR than patients with non-refractory disease (54% vs. 85%, p = 0.031). No differences in response rates according to the COO were observed. Twenty-eight patients (61%) underwent ASCT. At a median follow-up of 41 months, the estimated 3-year PFS and OS were 42% and 48%, respectively. The most common grade ≥3 adverse events were thrombocytopenia (70% of patients), neutropenia (67%) and anaemia (35%). There were no treatment-related deaths during LR-ESHAP cycles. In conclusion, LR-ESHAP is a feasible salvage regimen with promising efficacy results for patients with RR DLBCL.
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Affiliation(s)
- A Martín García-Sancho
- Hematology Department, Hospital Universitario de Salamanca-IBSAL, CIBERONC, Universidad de Salamanca, Salamanca, Spain
| | - M Baile
- Hematology Department, Hospital Universitario de Salamanca-IBSAL, CIBERONC, Universidad de Salamanca, Salamanca, Spain
| | - G Rodríguez
- Hematology Department, Hospital Universitario Virgen del Rocío/Virgen Macarena, Sevilla, Spain
| | - I Dlouhy
- Hematology Department, Hospital Clinic, Barcelona, Spain
| | - J M Sancho
- Hematology Department, Hospital Germans Trias i Pujol/ICO-IJC, Badalona, Spain
| | - I Jarque
- Hematology Department, Hospital Universitari i Plotècnic La Fe, CIBERONC, Valencia, Spain
| | - E González-Barca
- Institut Català d'Oncologia-Hospitalet, IDIBELL, Universitat de-Barcelona, Barcelona, Spain
| | - A Salar
- Hematology Department, Hospital del Mar, Barcelona, Spain
| | - M Espeso
- Hematology Department, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - C Grande
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - J Bergua
- Hematology Department, Hospital San Pedro de Alcántara, Cáceres, Spain
| | - S Montes-Moreno
- Pathology Department, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - A Redondo
- Hematology Department, Hospital Virgen del Puerto, Plasencia, Spain
| | - A Enjuanes
- Unidad de Genómica del IDIBAPS, Barcelona, Spain
| | - E Campo
- Pathology Department, Hospital Clinic, Barcelona, Spain
| | | | - D Caballero
- Hematology Department, Hospital Universitario de Salamanca-IBSAL, CIBERONC, Universidad de Salamanca, Salamanca, Spain
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3
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Frigola G, Bühler M, Marginet M, Enjuanes A, Nadeu F, Papaleo N, Salido M, Haralambieva E, Alamo J, Garcia-Bragado F, Álvarez R, Ramos R, Aldecoa I, Campo E, Colomo L, Balagué O. MYC and TP53 Alterations but Not MAPK Pathway Mutations Are Common Oncogenic Mechanisms in Follicular Dendritic Cell Sarcomas. Arch Pathol Lab Med 2023; 147:896-906. [PMID: 36355424 DOI: 10.5858/arpa.2021-0517-oa] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2022] [Indexed: 07/28/2023]
Abstract
CONTEXT.— Despite their stromal origin, follicular dendritic cells (FDCs) share many functions with hematopoietic system cells. FDC neoplasms are currently classified by the World Health Organization along with those of a histiocytic nature. However, the molecular alterations driving oncogenesis in FDC sarcomas (FDCSs) are beginning to be unveiled and do not seem to concur with those described in histiocytic neoplasms, namely MAPK pathway activation. OBJECTIVE.— To identify molecular alterations driving tumorigenesis in FDCS. DESIGN.— We investigated the role of MYC and TP53 in FDC-derived tumor oncogenesis and assessed comprehensively the status of the MAPK pathway in 16 FDCSs, 6 inflammatory pseudotumor (IPT)-like FDCSs, and 8 IPTs. RESULTS.— MYC structural alterations (both amplifications and rearrangements) were identified in 5 of 14 FDCSs (35.7%), all associated with MYC overexpression. TP53 mutations were identified in 4 of 14 FDCSs (28.6%), all of which displayed intense and diffuse p53 expression. None of these alterations were identified in any IPT-like FDCSs or in IPT cases. No MAPK pathway gene alterations were identified in any of the cases studied. CONCLUSIONS.— The presence of MYC and TP53 alterations and the lack of association with Epstein-Barr virus segregate classical FDCS from IPT-like FDCS, pointing at different oncogenic mechanisms in both entities. Our results suggest a possible oncogenic role of MYC and TP53 alterations in FDCS. The absence of MAPK pathway alterations confirms the lack of a significant role of this pathway in the oncogenesis of FDC-derived neoplasms.
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Affiliation(s)
- Gerard Frigola
- From the Department of Pathology, Hospital Clínic of Barcelona, Barcelona, Spain (Frigola, Bühler, Marginet, Alamo, Aldecoa, Campo, Balagué)
- The Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain (Frigola, Bühler, Enjuanes, Nadeu, Campo, Balagué)
| | - Marco Bühler
- From the Department of Pathology, Hospital Clínic of Barcelona, Barcelona, Spain (Frigola, Bühler, Marginet, Alamo, Aldecoa, Campo, Balagué)
- The Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain (Frigola, Bühler, Enjuanes, Nadeu, Campo, Balagué)
- The Department of Pathology, University Hospital Zürich, Zürich, Switzerland (Bühler, Haralambieva)
| | - Marta Marginet
- From the Department of Pathology, Hospital Clínic of Barcelona, Barcelona, Spain (Frigola, Bühler, Marginet, Alamo, Aldecoa, Campo, Balagué)
| | - Anna Enjuanes
- The Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain (Frigola, Bühler, Enjuanes, Nadeu, Campo, Balagué)
| | - Ferran Nadeu
- The Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain (Frigola, Bühler, Enjuanes, Nadeu, Campo, Balagué)
- The Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain (Nadeu, Campo, Balagué)
| | - Natalia Papaleo
- The Department of Pathology, Parc Taulí Hospital Universitari, Sabadell, Spain (Papaleo)
- The Department of Pathology, Hospital del Mar, Barcelona, Spain (Papaleo, Salido, Colomo)
- The Department of Diagnostic Fundamentals, University Pompeu Fabra, Barcelona, Spain (Papaleo, Colomo)
| | - Marta Salido
- The Department of Pathology, Hospital del Mar, Barcelona, Spain (Papaleo, Salido, Colomo)
| | - Eugenia Haralambieva
- The Department of Pathology, University Hospital Zürich, Zürich, Switzerland (Bühler, Haralambieva)
| | - José Alamo
- From the Department of Pathology, Hospital Clínic of Barcelona, Barcelona, Spain (Frigola, Bühler, Marginet, Alamo, Aldecoa, Campo, Balagué)
| | - Federico Garcia-Bragado
- The Department of Pathology, Complejo Hospitalario de Navarra, Pamplona, Spain (Garcia-Bragado)
| | - Ramiro Álvarez
- The Department of Pathology, Hospital Universitario Miguel Servet, Zaragoza, Spain (Álvarez)
| | - Rafael Ramos
- The Department of Pathology, Hospital Universitari Son Espases, Palma de Mallorca, Spain (Ramos)
| | - Iban Aldecoa
- From the Department of Pathology, Hospital Clínic of Barcelona, Barcelona, Spain (Frigola, Bühler, Marginet, Alamo, Aldecoa, Campo, Balagué)
| | - Elías Campo
- From the Department of Pathology, Hospital Clínic of Barcelona, Barcelona, Spain (Frigola, Bühler, Marginet, Alamo, Aldecoa, Campo, Balagué)
- The Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain (Frigola, Bühler, Enjuanes, Nadeu, Campo, Balagué)
- The Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain (Nadeu, Campo, Balagué)
- The Department of Clinical Fundamentals, University of Barcelona, Barcelona, Spain (Campo, Balagué)
| | - Lluis Colomo
- The Department of Pathology, Hospital del Mar, Barcelona, Spain (Papaleo, Salido, Colomo)
- The Department of Diagnostic Fundamentals, University Pompeu Fabra, Barcelona, Spain (Papaleo, Colomo)
| | - Olga Balagué
- From the Department of Pathology, Hospital Clínic of Barcelona, Barcelona, Spain (Frigola, Bühler, Marginet, Alamo, Aldecoa, Campo, Balagué)
- The Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain (Frigola, Bühler, Enjuanes, Nadeu, Campo, Balagué)
- The Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain (Nadeu, Campo, Balagué)
- The Department of Clinical Fundamentals, University of Barcelona, Barcelona, Spain (Campo, Balagué)
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4
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Grau M, López C, Navarro A, Frigola G, Nadeu F, Clot G, Bastidas G, Alcoceba M, Baptista MJ, Blanes M, Colomer D, Costa D, Domingo-Domenech E, Enjuanes A, Escoda L, Forcada P, Gine E, Lopez-Guerra M, Ramón O, Rivas-Delgado A, Vicente-Folch L, Wotherspoon A, Climent F, Campo E, López-Guillermo A, Matutes E, Beà S. Unraveling the genetics of transformed splenic marginal zone lymphoma. Blood Adv 2023:495159. [PMID: 36995085 PMCID: PMC10368783 DOI: 10.1182/bloodadvances.2022009415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/10/2023] [Accepted: 03/07/2023] [Indexed: 03/31/2023] Open
Abstract
The genetic mechanisms associated with splenic marginal zone lymphoma transformation (SMZL-T) are not well defined. We studied 41 SMZL patients that eventually underwent large B-cell lymphoma transformation. Tumor material was obtained only at diagnosis (9 patients), at diagnosis and transformation (18 patients), and only at transformation (14 patients). Samples were categorized in two groups: i) at diagnosis (SMZL, n=27 samples), and ii) at transformation (SMZL-T, n=32 samples). Using copy number arrays and a next-generation sequencing custom panel, we identified that the main genomic alterations in SMZL-T involved TNFAIP3, KMT2D, TP53, ARID1A, KLF2, 1q gains and losses of 9p21.3 (CDKN2A/B) and 7q31-q32. Compared with SMZL, SMZL-T had higher genomic complexity, and higher incidence of TNFAIP3 and TP53 alterations, 9p21.3 (CDKN2A/B) losses and 6p gains. SMZL and SMZL-T clones arose by divergent evolution from a common altered precursor cell which acquired different genetic alterations in virtually all evaluable cases (12/13, 92%). Using whole genome sequencing from diagnostic and transformation samples in one patient, we observed that the SMZL-T sample carried more genomic aberrations than the diagnostic sample, identified a translocation t(14;19)(q32;q13) present in both samples, and detected a focal B2M deletion due to chromothripsis acquired at transformation. Survival analysis showed that KLF2 mutations, complex karyotype and international prognostic index at transformation predicted for a shorter survival from transformation (P=0.001, P=0.042, and P=0.007, respectively). In summary, SMZL-T are characterized by higher genomic complexity than SMZL, and characteristic genomic alterations that could represent key players in the transformation event.
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Affiliation(s)
- Marta Grau
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Cristina López
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Alba Navarro
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | | | - Ferran Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Guillem Clot
- Institut d'Investigacions Biomediques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Miguel Alcoceba
- Department of Hematology, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Center for Cancer Research-IBMCC (USAL-CSIC), Salamanca, Spain
| | | | | | | | | | - Eva Domingo-Domenech
- Institut Catala d'Oncologia. Hospital Duran i Reynals, L'Hospitalet de Llobregat, Spain
| | | | | | - Pilar Forcada
- Hospital Universitari Mútua Terrassa, Terrassa, Spain
| | - Eva Gine
- Hospital Clinic de Barcelona, IDIBAPS, Barcelona, Spain
| | - Monica Lopez-Guerra
- Hospital Clinic of Barcelona; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Olga Ramón
- Hospital Universitario de Igualada, Igualada, Spain
| | | | | | | | - Fina Climent
- Hospital Universitari de Bellvitge-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Elías Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
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5
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Vegliante MC, Mazzara S, Zaccaria GM, De Summa S, Esposito F, Melle F, Motta G, Sapienza MR, Opinto G, Volpe G, Bucci A, Gargano G, Enjuanes A, Tabanelli V, Fiori S, Minoia C, Clemente F, Negri A, Gulino A, Morello G, Scattone A, Zito AF, Tommasi S, Agostinelli C, Vitolo U, Chiappella A, Barbui AM, Derenzini E, Zinzani PL, Casadei B, Rivas-Delgado A, López-Guillermo A, Campo E, Moschetta A, Guarini A, Pileri SA, Ciavarella S. NR1H3 (LXRα) is associated with pro-inflammatory macrophages, predicts survival and suggests potential therapeutic rationales in diffuse large b-cell lymphoma. Hematol Oncol 2022; 40:864-875. [PMID: 35850118 PMCID: PMC10087298 DOI: 10.1002/hon.3050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/06/2022] [Accepted: 07/14/2022] [Indexed: 12/13/2022]
Abstract
The role of macrophages (Mo) and their prognostic impact in diffuse large B-cell lymphomas (DLBCL) remain controversial. By regulating the lipid metabolism, Liver-X-Receptors (LXRs) control Mo polarization/inflammatory response, and their pharmacological modulation is under clinical investigation to treat human cancers, including lymphomas. Herein, we surveyed the role of LXRs in DLBCL for prognostic purposes. Comparing bulk tumors with purified malignant and normal B-cells, we found an intriguing association of NR1H3, encoding for the LXR-α isoform, with the tumor microenvironment (TME). CIBERSORTx-based purification on large DLBCL datasets revealed a high expression of the receptor transcript in M1-like pro-inflammatory Mo. By determining an expression cut-off of NR1H3, we used digital measurement to validate its prognostic capacity on two large independent on-trial and real-world cohorts. Independently of classical prognosticators, NR1H3high patients displayed longer survival compared with NR1H3low cases and a high-resolution Mo GEP dissection suggested a remarkable transcriptional divergence between subgroups. Overall, our findings indicate NR1H3 as a Mo-related biomarker identifying patients at higher risk and prompt future preclinical studies investigating its mouldability for therapeutic purposes.
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Affiliation(s)
| | - Saveria Mazzara
- Division of Hematopathology, European Institute of Oncology, IRCCS, Milan, Italy
| | - Gian Maria Zaccaria
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - Simona De Summa
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - Flavia Esposito
- Department of Mathematics, University of Bari Aldo Moro, Bari, Italy.,INDAM-GNCS Research Group, Rome, Italy
| | - Federica Melle
- Division of Hematopathology, European Institute of Oncology, IRCCS, Milan, Italy
| | - Giovanna Motta
- Division of Hematopathology, European Institute of Oncology, IRCCS, Milan, Italy
| | | | - Giuseppina Opinto
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - Giacomo Volpe
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - Antonella Bucci
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - Grazia Gargano
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy.,INDAM-GNCS Research Group, Rome, Italy
| | - Anna Enjuanes
- Unitat de Genòmica, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona; CIBERONC, Barcelona, Spain
| | - Valentina Tabanelli
- Division of Hematopathology, European Institute of Oncology, IRCCS, Milan, Italy
| | - Stefano Fiori
- Division of Hematopathology, European Institute of Oncology, IRCCS, Milan, Italy
| | - Carla Minoia
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - Felice Clemente
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - Antonio Negri
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - Alessandro Gulino
- Cogentech srl Società Benefit, FIRC Institute of Molecular Oncology (IFOM), Milan, Italy
| | - Gaia Morello
- Department of Health Sciences, Tumor Immunology Unit, University of Palermo School of Medicine, Palermo, Italy
| | - Anna Scattone
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - Alfredo F Zito
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - Stefania Tommasi
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - Claudio Agostinelli
- Haematopathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.,Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | | | - Annalisa Chiappella
- Division of Hematology and Stem Cell Transplantation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Anna Maria Barbui
- Department of Oncology and Hematology, Azienda Socio-Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy
| | - Enrico Derenzini
- Onco-Hematology Division, European Institute of Oncology IRCCS, Milan, Italy.,Department of Health Sciences, University of Milan, Milan, Italy
| | - Pier Luigi Zinzani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.,Istituto di Ematologia "Seràgnoli", IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Beatrice Casadei
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.,Istituto di Ematologia "Seràgnoli", IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Alfredo Rivas-Delgado
- CIBERONC, Barcelona, Spain; Hematology Department, Hospital Clínic, Barcelona; IDIBAPS, Barcelona, Spain
| | - Armando López-Guillermo
- CIBERONC, Barcelona, Spain; Hematology Department, Hospital Clínic, Barcelona; IDIBAPS, Barcelona, Spain
| | - Elias Campo
- CIBERONC, Barcelona, Spain; Haematopathology Unit, Pathology Department, Hospital Clínic, Barcelona; University of Barcelona, Barcelona, Spain
| | - Antonio Moschetta
- Department of Interdisciplinary Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Attilio Guarini
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - Stefano A Pileri
- Division of Hematopathology, European Institute of Oncology, IRCCS, Milan, Italy
| | - Sabino Ciavarella
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
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6
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Nadeu F, Royo R, Massoni-Badosa R, Playa-Albinyana H, Garcia-Torre B, Duran-Ferrer M, Dawson KJ, Kulis M, Diaz-Navarro A, Villamor N, Melero JL, Chapaprieta V, Dueso-Barroso A, Delgado J, Moia R, Ruiz-Gil S, Marchese D, Giró A, Verdaguer-Dot N, Romo M, Clot G, Rozman M, Frigola G, Rivas-Delgado A, Baumann T, Alcoceba M, González M, Climent F, Abrisqueta P, Castellví J, Bosch F, Aymerich M, Enjuanes A, Ruiz-Gaspà S, López-Guillermo A, Jares P, Beà S, Capella-Gutierrez S, Gelpí JL, López-Bigas N, Torrents D, Campbell PJ, Gut I, Rossi D, Gaidano G, Puente XS, Garcia-Roves PM, Colomer D, Heyn H, Maura F, Martín-Subero JI, Campo E. Detection of early seeding of Richter transformation in chronic lymphocytic leukemia. Nat Med 2022; 28:1662-1671. [PMID: 35953718 PMCID: PMC9388377 DOI: 10.1038/s41591-022-01927-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 07/01/2022] [Indexed: 02/06/2023]
Abstract
Richter transformation (RT) is a paradigmatic evolution of chronic lymphocytic leukemia (CLL) into a very aggressive large B cell lymphoma conferring a dismal prognosis. The mechanisms driving RT remain largely unknown. We characterized the whole genome, epigenome and transcriptome, combined with single-cell DNA/RNA-sequencing analyses and functional experiments, of 19 cases of CLL developing RT. Studying 54 longitudinal samples covering up to 19 years of disease course, we uncovered minute subclones carrying genomic, immunogenetic and transcriptomic features of RT cells already at CLL diagnosis, which were dormant for up to 19 years before transformation. We also identified new driver alterations, discovered a new mutational signature (SBS-RT), recognized an oxidative phosphorylation (OXPHOS)high–B cell receptor (BCR)low-signaling transcriptional axis in RT and showed that OXPHOS inhibition reduces the proliferation of RT cells. These findings demonstrate the early seeding of subclones driving advanced stages of cancer evolution and uncover potential therapeutic targets for RT. Single-cell genomic and transcriptomic analyses of longitudinal samples of patients with Richter syndrome reveal the presence and dynamics of clones driving transformation from chronic lymphocytic leukemia years before clinical manifestation
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Affiliation(s)
- Ferran Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Romina Royo
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Ramon Massoni-Badosa
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Heribert Playa-Albinyana
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Beatriz Garcia-Torre
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Martí Duran-Ferrer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Marta Kulis
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Ander Diaz-Navarro
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Neus Villamor
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain
| | | | - Vicente Chapaprieta
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Julio Delgado
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Riccardo Moia
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Sara Ruiz-Gil
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Domenica Marchese
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ariadna Giró
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Núria Verdaguer-Dot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Mónica Romo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Guillem Clot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Maria Rozman
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain
| | | | - Alfredo Rivas-Delgado
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain
| | - Tycho Baumann
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Miguel Alcoceba
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Biología Molecular e Histocompatibilidad, IBSAL-Hospital Universitario, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Marcos González
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Biología Molecular e Histocompatibilidad, IBSAL-Hospital Universitario, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Fina Climent
- Hospital Universitari de Bellvitge-Institut d'Investigació Biomédica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Pau Abrisqueta
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Josep Castellví
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Francesc Bosch
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Marta Aymerich
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain
| | - Anna Enjuanes
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Sílvia Ruiz-Gaspà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Armando López-Guillermo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Pedro Jares
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Sílvia Beà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | | | - Josep Ll Gelpí
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Núria López-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - David Torrents
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Davide Rossi
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Xose S Puente
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Pablo M Garcia-Roves
- Universitat de Barcelona, Barcelona, Spain.,Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Dolors Colomer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Francesco Maura
- Myeloma Service, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - José I Martín-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Universitat de Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Elías Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain. .,Hospital Clínic of Barcelona, Barcelona, Spain. .,Universitat de Barcelona, Barcelona, Spain.
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7
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Rivas-Delgado A, Nadeu F, Andrade-Campos M, López C, Enjuanes A, Mozas P, Frigola G, Colomo L, Sanchez-Gonzalez B, Villamor N, Beà S, Campo E, Salar A, Giné E, López-Guillermo A, Bellosillo B. Cell-Free DNA for Genomic Analysis in Primary Mediastinal Large B-Cell Lymphoma. Diagnostics (Basel) 2022; 12:diagnostics12071575. [PMID: 35885481 PMCID: PMC9324191 DOI: 10.3390/diagnostics12071575] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022] Open
Abstract
High-throughput sequencing of cell-free DNA (cfDNA) has emerged as a promising noninvasive approach in lymphomas, being particularly useful when a biopsy specimen is not available for molecular analysis, as it frequently occurs in primary mediastinal large B-cell lymphoma (PMBL). We used cfDNA for genomic characterization in 20 PMBL patients by means of a custom NGS panel for gene mutations and low-pass whole-genome sequencing (WGS) for copy number analysis (CNA) in a real-life setting. Appropriate cfDNA to perform the analyses was obtained in 18/20 cases. The sensitivity of cfDNA to detect the mutations present in paired FFPE samples was 69% (95% CI: 60–78%). The mutational landscape found in cfDNA samples was highly consistent with that of the tissue, with the most frequently mutated genes being B2M (61%), SOCS1 (61%), GNA13 (44%), STAT6 (44%), NFKBIA (39%), ITPKB (33%), and NFKBIE (33%). Overall, we observed a 75% concordance to detect CNA gains/losses between DNA microarray and low-pass WGS. The sensitivity of low-pass WGS was remarkably higher for clonal CNA (18/20, 90%) compared to subclonal alterations identified by DNA microarray. No significant associations between cfDNA amount and tumor burden or outcome were found. cfDNA is an excellent alternative source for the accurate genetic characterization of PMBL cases.
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Affiliation(s)
- Alfredo Rivas-Delgado
- Hematology Department, Hospital Clínic de Barcelona, 08036 Barcelona, Spain; (P.M.); (E.G.); (A.L.-G.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (F.N.); (C.L.); (A.E.); (N.V.); (S.B.); (E.C.)
- Faculty of Medicine and Health Sciences, Universitat de Barcelona, 08007 Barcelona, Spain
- Correspondence: ; Tel.: +34-932275428
| | - Ferran Nadeu
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (F.N.); (C.L.); (A.E.); (N.V.); (S.B.); (E.C.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Marcio Andrade-Campos
- Hematology Department, Hospital del Mar-IMIM, 08003 Barcelona, Spain; (M.A.-C.); (B.S.-G.); (A.S.)
- Grup de Recerca Clínica, Aplicada en Neoplàsies Hematològiques-Hospital del Mar-IMIM, 08003 Barcelona, Spain;
| | - Cristina López
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (F.N.); (C.L.); (A.E.); (N.V.); (S.B.); (E.C.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Anna Enjuanes
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (F.N.); (C.L.); (A.E.); (N.V.); (S.B.); (E.C.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Pablo Mozas
- Hematology Department, Hospital Clínic de Barcelona, 08036 Barcelona, Spain; (P.M.); (E.G.); (A.L.-G.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (F.N.); (C.L.); (A.E.); (N.V.); (S.B.); (E.C.)
| | - Gerard Frigola
- Hematopathology Section, Pathology Department, Hospital Clínic de Barcelona, 08036 Barcelona, Spain;
| | - Luis Colomo
- Pathology Department, Hospital del Mar-IMIM, 08003 Barcelona, Spain;
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08002 Barcelona, Spain
| | - Blanca Sanchez-Gonzalez
- Hematology Department, Hospital del Mar-IMIM, 08003 Barcelona, Spain; (M.A.-C.); (B.S.-G.); (A.S.)
- Grup de Recerca Clínica, Aplicada en Neoplàsies Hematològiques-Hospital del Mar-IMIM, 08003 Barcelona, Spain;
| | - Neus Villamor
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (F.N.); (C.L.); (A.E.); (N.V.); (S.B.); (E.C.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
- Hematopathology Section, Pathology Department, Hospital Clínic de Barcelona, 08036 Barcelona, Spain;
| | - Sílvia Beà
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (F.N.); (C.L.); (A.E.); (N.V.); (S.B.); (E.C.)
- Faculty of Medicine and Health Sciences, Universitat de Barcelona, 08007 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
- Hematopathology Section, Pathology Department, Hospital Clínic de Barcelona, 08036 Barcelona, Spain;
| | - Elías Campo
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (F.N.); (C.L.); (A.E.); (N.V.); (S.B.); (E.C.)
- Faculty of Medicine and Health Sciences, Universitat de Barcelona, 08007 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
- Hematopathology Section, Pathology Department, Hospital Clínic de Barcelona, 08036 Barcelona, Spain;
| | - Antonio Salar
- Hematology Department, Hospital del Mar-IMIM, 08003 Barcelona, Spain; (M.A.-C.); (B.S.-G.); (A.S.)
- Grup de Recerca Clínica, Aplicada en Neoplàsies Hematològiques-Hospital del Mar-IMIM, 08003 Barcelona, Spain;
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08002 Barcelona, Spain
| | - Eva Giné
- Hematology Department, Hospital Clínic de Barcelona, 08036 Barcelona, Spain; (P.M.); (E.G.); (A.L.-G.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (F.N.); (C.L.); (A.E.); (N.V.); (S.B.); (E.C.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Armando López-Guillermo
- Hematology Department, Hospital Clínic de Barcelona, 08036 Barcelona, Spain; (P.M.); (E.G.); (A.L.-G.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (F.N.); (C.L.); (A.E.); (N.V.); (S.B.); (E.C.)
- Faculty of Medicine and Health Sciences, Universitat de Barcelona, 08007 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Beatriz Bellosillo
- Grup de Recerca Clínica, Aplicada en Neoplàsies Hematològiques-Hospital del Mar-IMIM, 08003 Barcelona, Spain;
- Pathology Department, Hospital del Mar-IMIM, 08003 Barcelona, Spain;
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08002 Barcelona, Spain
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8
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Nadeu F, Royo R, Massoni-Badosa R, Garcia-Torre B, Duran-Ferrer M, Dawson KJ, Kulis M, Diaz-Navarro A, Villamor N, Melero JL, Chapaprieta V, Dueso-Barroso A, Delgado J, Moia R, Ruiz-Gil S, Marchese D, Verdaguer-Dot N, Romo M, Rozman M, Frigola G, Rivas-Delgado A, Baumann T, Alcoceba M, González M, Climent F, Abrisqueta P, Castellví J, Bosch F, Aymerich M, Enjuanes A, Ruiz-Gaspà S, López-Guillermo A, Jares P, Beà S, Colomer D, López-Bigas N, LlGelpí J, Torrents D, Campbell PJ, Gut I, Garcia-Roves PM, Rossi D, Gaidano G, Puente XS, Heyn H, Maura F, Martín-Subero JI, Campo E. Abstract 3795: Early seeding of Richter transformation in chronic lymphocytic leukemia. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3795] [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: Clonal evolution drives cancer development due to the emergence and/or selection of proliferatively advantageous subclones. Its understanding may facilitate the design of anticipation-based management strategies. Richter transformation (RT) is a paradigmatic tumor evolution in which chronic lymphocytic leukemia (CLL), an indolent neoplasia of mature B-cells, transforms into a high-grade lymphoma, usually diffuse large B-cell lymphoma (DLBCL), conferring a dismal prognosis. The evolutionary trajectories of RT and its driving (epi)genomic mechanisms remain largely unknown.
Aims: To reconstruct the evolutionary history of RT and to reveal the molecular processes underlying this transformation.
Methods: We characterized the whole genome (WGS), epigenome (DNA methylation, H3K27ac, ATAC-seq), and transcriptome (RNA-seq), combined with single-cell DNA and RNA sequencing analyses, of 19 CLL patients developing RT before (n=3) or after treatment with chemoimmunotherapy (n=6) and targeted therapies (BCR or BCL2 inhibitors, n=10). We analyzed 54 longitudinal samples covering up to 19 years of disease course.
Results: Our WGS analyses uncovered that RT is characterized by a remarkable structural complexity. We also identified a novel treatment-independent RT-specific mutational process, which we named SBS-RT. The genetic driver landscape of RT is a compendium of alterations in genes involved in cell cycle, MYC, and NF-κB pathways, frequently targeted in single catastrophic events including chromothripsis and chromoplexy. The WGS-based phylogenic reconstruction and single-cell DNA/RNA-seq analyses identified a very early diversification of CLL leading to emergence of RT-cells carrying specific genetic drivers and transcriptomic profiles of RT already at CLL diagnosis. These small subclones were dormant for 6-19 years until rapid expansion associated with the clinical transformation. While the DNA methylome kept track of the cell of origin and proliferative history of RT cells, their chromatin configuration and transcriptional program converged into the overexpression of cell cycle regulators, Toll-like receptors, MYC, MTORC1, and OXPHOS related transcripts, as well as downregulation of BCR pathway. This phenotypic shift was related to de novo activation of key transcription factors. In vitro experiments confirmed that RT cells have a 4-fold higher oxygen consumption at routine respiration and electron transfer system capacity compared to CLL. The resistance of RT to BCR inhibition is consistent with its high OXPHOS and low BCR signaling, which mimics de novo DLBCL-OXPHOS insensitive to BCR inhibition. This OXPHOShigh-BCRlow transcriptional axis of RT can be exploited therapeutically.
Conclusions: These findings demonstrate the early seeding of subclones driving advanced stages of cancer evolution and uncover therapeutic targets for the, once expanded, lethal Richter transformation.
Citation Format: Ferran Nadeu, Romina Royo, Ramon Massoni-Badosa, Beatriz Garcia-Torre, Martí Duran-Ferrer, Kevin J. Dawson, Marta Kulis, Ander Diaz-Navarro, Neus Villamor, Juan L. Melero, Vicente Chapaprieta, Ana Dueso-Barroso, Julio Delgado, Riccardo Moia, Sara Ruiz-Gil, Domenica Marchese, Núria Verdaguer-Dot, Mónica Romo, Maria Rozman, Gerard Frigola, Alfredo Rivas-Delgado, Tycho Baumann, Miguel Alcoceba, Marcos González, Fina Climent, Pau Abrisqueta, Josep Castellví, Francesc Bosch, Marta Aymerich, Anna Enjuanes, Sílvia Ruiz-Gaspà, Armando López-Guillermo, Pedro Jares, Sílvia Beà, Dolors Colomer, Núria López-Bigas, Josep LlGelpí, David Torrents, Peter J. Campbell, Ivo Gut, Pablo M. Garcia-Roves, Davide Rossi, Gianluca Gaidano, Xose S. Puente, Holger Heyn, Francesco Maura, José I. Martín-Subero, Elías Campo. Early seeding of Richter transformation in chronic lymphocytic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3795.
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Affiliation(s)
- Ferran Nadeu
- 1Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Romina Royo
- 2Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Ramon Massoni-Badosa
- 3CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Beatriz Garcia-Torre
- 1Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Martí Duran-Ferrer
- 1Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Marta Kulis
- 1Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Ander Diaz-Navarro
- 5Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | | | | | - Vicente Chapaprieta
- 1Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | | | | | - Sara Ruiz-Gil
- 3CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Domenica Marchese
- 3CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Núria Verdaguer-Dot
- 1Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Mónica Romo
- 1Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | | | | | | | - Miguel Alcoceba
- 9IBSAL-Hospital Universitario, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Marcos González
- 9IBSAL-Hospital Universitario, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Fina Climent
- 10Hospital Universitari de Bellvitge-Institut d'Investigació Biomédica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Spain
| | - Pau Abrisqueta
- 11Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Josep Castellví
- 11Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Francesc Bosch
- 11Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | | | - Anna Enjuanes
- 1Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Sílvia Ruiz-Gaspà
- 1Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Pedro Jares
- 6Hospital Clínic of Barcelona, Barcelona, Spain
| | - Sílvia Beà
- 6Hospital Clínic of Barcelona, Barcelona, Spain
| | | | - Núria López-Bigas
- 12Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Josep LlGelpí
- 2Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - David Torrents
- 2Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | | | - Ivo Gut
- 3CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Pablo M. Garcia-Roves
- 13Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Spain
| | - Davide Rossi
- 14Oncology Institute of Southern Switzerlan, Bellinzona, Switzerland
| | | | - Xose S. Puente
- 5Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Holger Heyn
- 3CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Francesco Maura
- 15Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - José I. Martín-Subero
- 1Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Elías Campo
- 1Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
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9
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Dlouhy I, Karube K, Enjuanes A, Salaverria I, Nadeu F, Ramis-Zaldivar JE, Valero JG, Rivas-Delgado A, Magnano L, Martin-García D, Pérez-Galán P, Clot G, Rovira J, Jares P, Balagué O, Giné E, Mozas P, Briones J, Sancho JM, Salar A, Mercadal S, Alcoceba M, Valera A, Campo E, López-Guillermo A. Revised International Prognostic Index and genetic alterations are associated with early failure to R-CHOP in patients with diffuse large B-cell lymphoma. Br J Haematol 2021; 196:589-598. [PMID: 34632572 DOI: 10.1111/bjh.17858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/26/2021] [Accepted: 09/12/2021] [Indexed: 11/28/2022]
Abstract
Relapsed or refractory diffuse large B-cell lymphoma (DLBCL) cases have a poor outcome. Here we analysed clinico-biological features in 373 DLBCL patients homogeneously treated with rituximab, cyclophosphamide, doxorubicin, vincristine and prednisolone (R-CHOP), in order to identify variables associated with early failure to treatment (EF), defined as primary refractoriness or relapse within 12 months from diagnosis. In addition to clinical features, mutational status of 106 genes was studied by targeted next-generation sequencing in 111 cases, copy number alterations in 87, and gene expression profile (GEP) in 39. Ninety-seven cases (26%) were identified as EF and showed significantly shorter overall survival (OS). Patients with B symptoms, advanced stage, high levels of serum lactate dehydrogenase (LDH) or β2-microglobulin, low lymphocyte/monocyte ratio and higher Revised International Prognostic Index (R-IPI) scores, as well as those with BCL2 rearrangements more frequently showed EF, with R-IPI being the most important in logistic regression. Mutations in NOTCH2, gains in 5p15·33 (TERT), 12q13 (CDK2), 12q14·1 (CDK4) and 12q15 (MDM2) showed predictive importance for EF independently from R-IPI. GEP studies showed that EF cases were significantly enriched in sets related to cell cycle regulation and inflammatory response, while cases in response showed over-representation of gene sets related to extra-cellular matrix and tumour microenvironment.
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Affiliation(s)
- Ivan Dlouhy
- Department of Hematology, Hospital Clínic, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Tumores Hematológicos, Madrid, Spain
| | - Kennosuke Karube
- Institut d`Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Cell Biology & Pathology Department, University of the Ryukyus Graduate School of Medicine, Okinawa, Japan
| | - Anna Enjuanes
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Tumores Hematológicos, Madrid, Spain.,Institut d`Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Itziar Salaverria
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Tumores Hematológicos, Madrid, Spain.,Institut d`Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Ferran Nadeu
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Tumores Hematológicos, Madrid, Spain.,Institut d`Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Juan Enric Ramis-Zaldivar
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Tumores Hematológicos, Madrid, Spain.,Institut d`Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Juan G Valero
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Tumores Hematológicos, Madrid, Spain.,Institut d`Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Alfredo Rivas-Delgado
- Department of Hematology, Hospital Clínic, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Tumores Hematológicos, Madrid, Spain
| | - Laura Magnano
- Department of Hematology, Hospital Clínic, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Tumores Hematológicos, Madrid, Spain
| | - David Martin-García
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Tumores Hematológicos, Madrid, Spain.,Institut d`Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Patricia Pérez-Galán
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Tumores Hematológicos, Madrid, Spain.,Institut d`Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Guillem Clot
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Tumores Hematológicos, Madrid, Spain.,Institut d`Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Jordina Rovira
- Department of Hematology, Hospital Clínic, Barcelona, Spain
| | - Pedro Jares
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Tumores Hematológicos, Madrid, Spain.,Institut d`Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Olga Balagué
- Institut d`Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Eva Giné
- Department of Hematology, Hospital Clínic, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Tumores Hematológicos, Madrid, Spain
| | - Pablo Mozas
- Department of Hematology, Hospital Clínic, Barcelona, Spain
| | | | | | | | | | - Miguel Alcoceba
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Tumores Hematológicos, Madrid, Spain.,Hospital Clínico Universitario, Salamanca, Spain
| | - Alexandra Valera
- Institut d`Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Elías Campo
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Tumores Hematológicos, Madrid, Spain.,Institut d`Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,University of Barcelona, Barcelona, Spain
| | - Armando López-Guillermo
- Department of Hematology, Hospital Clínic, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Tumores Hematológicos, Madrid, Spain.,University of Barcelona, Barcelona, Spain
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10
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Ramis-Zaldivar JE, Gonzalez-Farre B, Nicolae A, Pack S, Clot G, Nadeu F, Mottok A, Horn H, Song JY, Fu K, Wright G, Gascoyne RD, Chan WC, Scott DW, Feldman AL, Valera A, Enjuanes A, Braziel RM, Smeland EB, Staudt LM, Rosenwald A, Rimsza LM, Ott G, Jaffe ES, Salaverria I, Campo E. MAP-kinase and JAK-STAT pathways dysregulation in plasmablastic lymphoma. Haematologica 2021; 106:2682-2693. [PMID: 33951889 PMCID: PMC8485662 DOI: 10.3324/haematol.2020.271957] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [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: 09/24/2020] [Indexed: 11/09/2022] Open
Abstract
Plasmablastic lymphoma (PBL) is an aggressive B-cell lymphoma with an immunoblastic/large cell morphology and plasmacytic differentiation. The differential diagnosis with Burkitt lymphoma (BL), plasma cell myeloma (PCM) and some variants of diffuse large B-cell lymphoma (DLBCL) may be challenging due to the overlapping morphological, genetic and immunophenotypic features. Furthermore, the genomic landscape in PBL is not well known. To characterize the genetic and molecular heterogeneity of these tumors, we investigated thirty-four PBL using an integrated approach, including fluorescence in situ hybridization, targeted sequencing of 94 B-cell lymphoma related genes, and copy-number arrays. PBL were characterized by high genetic complexity including MYC translocations (87%), gains of 1q21.1-q44, trisomy 7, 8q23.2-q24.21, 11p13-p11.2, 11q14.2-q25, 12p and 19p13.3-p13.13, losses of 1p33, 1p31.1-p22.3, 13q and 17p13.3-p11.2, and recurrent mutations of STAT3 (37%), NRAS and TP53 (33%), MYC and EP300 (19%) and CARD11, SOCS1 and TET2 (11%). Pathway enrichment analysis suggested a cooperative action between MYC alterations and MAPK (49%) and JAK-STAT (40%) signaling pathways. Of note, EBVnegative PBL cases had higher mutational and copy-number load and more frequent TP53, CARD11 and MYC mutations, whereas EBV-positive PBL tended to have more mutations affecting the JAK-STAT pathway. In conclusion, these findings further unravel the distinctive molecular heterogeneity of PBL identifying novel molecular targets and the different genetic profile of these tumors related to EBV infection.
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Affiliation(s)
- Joan Enric Ramis-Zaldivar
- Hematopathology Unit, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid
| | - Blanca Gonzalez-Farre
- Hematopathology Unit, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid
| | - Alina Nicolae
- Hematopathology Section, Laboratory of Pathology, National Cancer Institute, Bethesda
| | - Svetlana Pack
- Hematopathology Section, Laboratory of Pathology, National Cancer Institute, Bethesda
| | - Guillem Clot
- Hematopathology Unit, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid
| | - Ferran Nadeu
- Hematopathology Unit, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid
| | - Anja Mottok
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver
| | - Heike Horn
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, Stuttgart, and Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, and University of Tübingen
| | - Joo Y Song
- Department of Pathology, City of Hope National Medical Center, Duarte
| | - Kai Fu
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | - George Wright
- Biometric Research Branch, Division of Cancer Diagnosis and Treatment, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Randy D Gascoyne
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver
| | - Wing C Chan
- Department of Pathology, City of Hope National Medical Center, Duarte
| | - David W Scott
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Department of Medicine, University of British Columbia, Vancouver
| | - Andrew L Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Alexandra Valera
- Hematopathology Unit, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona
| | - Anna Enjuanes
- Hematopathology Unit, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid
| | - Rita M Braziel
- Department of Clinical Pathology, Oregon Health and Science University, Oregon
| | - Erlend B Smeland
- Department of Immunology and Centre for Cancer Biomedicine, University of Oslo and Oslo University Hospital, Oslo
| | - Louis M Staudt
- Lymphoid Malignancies Branch, Center for Cancer Research, National Institutes of Health, Bethesda
| | | | - Lisa M Rimsza
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Phoenix
| | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, Stuttgart, and Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, and University of Tübingen
| | - Elaine S Jaffe
- Hematopathology Section, Laboratory of Pathology, National Cancer Institute, Bethesda
| | - Itziar Salaverria
- Hematopathology Unit, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid
| | - Elias Campo
- Hematopathology Unit, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid.
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11
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Sutton LA, Ljungström V, Enjuanes A, Cortese D, Skaftason A, Tausch E, Stano Kozubik K, Nadeu F, Armand M, Malcikova J, Pandzic T, Forster J, Davis Z, Oscier D, Rossi D, Ghia P, Strefford JC, Pospisilova S, Stilgenbauer S, Davi F, Campo E, Stamatopoulos K, Rosenquist R, On Behalf Of The European Research Initiative On Cll Eric. Comparative analysis of targeted next-generation sequencing panels for the detection of gene mutations in chronic lymphocytic leukemia: an ERIC multi-center study. Haematologica 2021; 106:682-691. [PMID: 32273480 PMCID: PMC7927885 DOI: 10.3324/haematol.2019.234716] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 02/11/2020] [Indexed: 12/12/2022] Open
Abstract
Next-generation sequencing (NGS) has transitioned from research to clinical routine, yet the comparability of different technologies for mutation profiling remains an open question. We performed a European multicenter (n=6) evaluation of three amplicon-based NGS assays targeting 11 genes recurrently mutated in chronic lymphocytic leukemia. Each assay was assessed by two centers using 48 pre-characterized chronic lymphocytic leukemia samples; libraries were sequenced on the Illumina MiSeq instrument and bioinformatics analyses were centralized. Across all centers the median percentage of target reads ≥100x ranged from 94.2-99.8%. In order to rule out assay-specific technical variability, we first assessed variant calling at the individual assay level i.e., pairwise analysis of variants detected amongst partner centers. After filtering for variants present in the paired normal sample and removal of PCR/sequencing artefacts, the panels achieved 96.2% (Multiplicom), 97.7% (TruSeq) and 90% (HaloPlex) concordance at a variant allele frequency (VAF) >0.5%. Reproducibility was assessed by looking at the inter-laboratory variation in detecting mutations and 107 of 115 (93% concordance) mutations were detected by all six centers, while the remaining eight variants (7%) were undetected by a single center. Notably, 6 of 8 of these variants concerned minor subclonal mutations (VAF <5%). We sought to investigate low-frequency mutations further by using a high-sensitivity assay containing unique molecular identifiers, which confirmed the presence of several minor subclonal mutations. Thus, while amplicon-based approaches can be adopted for somatic mutation detection with VAF >5%, after rigorous validation, the use of unique molecular identifiers may be necessary to reach a higher sensitivity and ensure consistent and accurate detection of low-frequency variants.
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Affiliation(s)
- Lesley-Ann Sutton
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Viktor Ljungström
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Enjuanes
- Institut d’Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain and Hospital Clínic of Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Diego Cortese
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Aron Skaftason
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Eugen Tausch
- Department of Internal Medicine III, Ulm University,Ulm, Germany
| | - Katerina Stano Kozubik
- Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ferran Nadeu
- Institut d’Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain and Hospital Clínic of Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Marine Armand
- AP-HP, Hopital Pitie-Salpetriere, Department of Hematology, Sorbonne Université, Paris, France
| | - Jikta Malcikova
- Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jade Forster
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Zadie Davis
- Department of Hematology, Royal Bournemouth Hospital, Bournemouth, UK
| | - David Oscier
- Department of Hematology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Davide Rossi
- Hematology Department, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Paolo Ghia
- Division of Experimental Oncology, Università Vita-Salute San Raffaele and IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Jonathan C Strefford
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sarka Pospisilova
- Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | - Frederic Davi
- AP-HP, Hopital Pitie-Salpetriere, Department of Hematology, Sorbonne Université, Paris, France
| | - Elias Campo
- Institut d’Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain and Hospital Clínic of Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Kostas Stamatopoulos
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden,Institute of Applied Biosciences, Center for Research and Technology, Thessaloniki, Greec
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden,Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
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12
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Demajo S, Albero R, Clot G, Castellano G, Navarro A, Capdevila C, Enjuanes A, Nadeu F, Giné E, Pinyol M, Jaffe ES, Ott G, Staudt LM, Rosenwald A, Scott DW, Rimsza LM, López-Guillermo A, Beà S, Campo E, Jares P. A Cyclin D1-Dependent Transcriptional Program Predicts Clinical Outcome in Mantle Cell Lymphoma. Clin Cancer Res 2021; 27:213-225. [PMID: 33046520 PMCID: PMC8051616 DOI: 10.1158/1078-0432.ccr-20-2868] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/16/2020] [Accepted: 10/07/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Mantle cell lymphoma (MCL) is characterized by the t(11;14)(q13;q32) translocation leading to cyclin D1 overexpression. Cyclin D1 is a major cell-cycle regulator and also regulates transcription, but the impact of cyclin D1-mediated transcriptional dysregulation on MCL pathogenesis remains poorly understood. The aim of this study was to define a cyclin D1-dependent gene expression program and analyze its prognostic value. EXPERIMENTAL DESIGN We integrated genome-wide expression analysis of cyclin D1-silenced and overexpressing cells with cyclin D1 chromatin-binding profiles to identify a cyclin D1-dependent transcriptional program in MCL cells. We analyzed this gene program in two MCL series of peripheral blood samples (n = 53) and lymphoid tissues (n = 106) to determine its biological and clinical relevance. We then obtained a simplified signature of this program and evaluated a third series of peripheral blood MCL samples (n = 81) by NanoString gene expression profiling to validate our findings. RESULTS We identified a cyclin D1-dependent transcriptional program composed of 295 genes that were mainly involved in cell-cycle control. The cyclin D1-dependent gene program was overexpressed in MCL tumors directly proportional to cyclin D1 levels. High expression of this program conferred an adverse prognosis with significant shorter overall survival of the patients. These observations were validated in an independent cohort of patients using a simplified 37-gene cyclin D1 signature. The cyclin D1-dependent transcriptional program was also present in multiple myeloma and breast tumors with cyclin D1 overexpression. CONCLUSIONS We identified a cyclin D1-dependent transcriptional program that is overexpressed in MCL and predicts clinical outcome.
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Affiliation(s)
- Santiago Demajo
- Lymphoid Neoplasm Program, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- Department of Pathology and Experimental Therapeutics, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Robert Albero
- Lymphoid Neoplasm Program, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Guillem Clot
- Lymphoid Neoplasm Program, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Alba Navarro
- Lymphoid Neoplasm Program, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Cristina Capdevila
- Lymphoid Neoplasm Program, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Anna Enjuanes
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Genomics Unit, IDIBAPS, Barcelona, Spain
| | - Ferran Nadeu
- Lymphoid Neoplasm Program, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Eva Giné
- Lymphoid Neoplasm Program, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Magda Pinyol
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Genomics Unit, IDIBAPS, Barcelona, Spain
| | | | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus and Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Louis M Staudt
- Center for Cancer Research, Lymphoid Malignancies Branch, NCI, Bethesda, Maryland
| | | | - David W Scott
- Centre for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Lisa M Rimsza
- Department of Pathology, Mayo Clinic, Scottsdale, Arizona
| | - Armando López-Guillermo
- Lymphoid Neoplasm Program, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- Hematology Department, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Sílvia Beà
- Lymphoid Neoplasm Program, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Elias Campo
- Lymphoid Neoplasm Program, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematopathology Unit, Department of Anatomic Pathology, Hospital Clinic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Pedro Jares
- Lymphoid Neoplasm Program, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematopathology Unit, Department of Anatomic Pathology, Hospital Clinic of Barcelona, University of Barcelona, Barcelona, Spain
- Molecular Biology Core, Hospital Clinic of Barcelona, Barcelona, Spain
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13
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Rivas-Delgado A, Nadeu F, Enjuanes A, Casanueva-Eliceiry S, Mozas P, Magnano L, Castrejón de Anta N, Rovira J, Dlouhy I, Martín S, Osuna M, Rodríguez S, Simó M, Pinyol M, Baumann T, Beà S, Balagué O, Delgado J, Villamor N, Setoain X, Campo E, Giné E, López-Guillermo A. Mutational Landscape and Tumor Burden Assessed by Cell-free DNA in Diffuse Large B-Cell Lymphoma in a Population-Based Study. Clin Cancer Res 2020; 27:513-521. [PMID: 33122345 DOI: 10.1158/1078-0432.ccr-20-2558] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/29/2020] [Accepted: 10/26/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE We analyzed the utility of cell-free DNA (cfDNA) in a prospective population-based cohort to determine the mutational profile, assess tumor burden, and estimate its impact in response rate and outcome in patients with diffuse large B-cell lymphoma (DLBCL). EXPERIMENTAL DESIGN A total of 100 patients were diagnosed with DLBCL during the study period. Mutational status of 112 genes was studied in cfDNA by targeted next-generation sequencing. Paired formalin-fixed, paraffin-embedded samples and volumetric PET/CT were assessed when available. RESULTS Appropriate cfDNA to perform the analyses was obtained in 79 of 100 cases. At least one mutation could be detected in 69 of 79 cases (87%). The sensitivity of cfDNA to detect the mutations was 68% (95% confidence interval, 56.2-78.7). The mutational landscape found in cfDNA samples was highly consistent with that shown in the tissue and allowed genetic classification in 43% of the cases. A higher amount of circulating tumor DNA (ctDNA) significantly correlated with clinical parameters related to tumor burden (elevated lactate dehydrogenase and β2-microglobulin serum levels, advanced stage, and high-risk International Prognostic Index) and total metabolic tumor volume assessed by PET/CT. In patients treated with curative intent, high ctDNA levels (>2.5 log hGE/mL) were associated with lower complete response (65% vs. 96%; P < 0.004), shorter progression-free survival (65% vs. 85%; P = 0.038), and overall survival (73% vs. 100%; P = 0.007) at 2 years, although it did not maintain prognostic value in multivariate analyses. CONCLUSIONS In a population-based prospective DLBCL series, cfDNA resulted as an alternative source to estimate tumor burden and to determine the tumor mutational profile and genetic classification, which have prognostic implications and may contribute to a future tailored treatment.
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Affiliation(s)
- Alfredo Rivas-Delgado
- Department of Hematology, Hospital Clínic de Barcelona, Barcelona, Spain. .,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Ferran Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Anna Enjuanes
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | | | - Pablo Mozas
- Department of Hematology, Hospital Clínic de Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Laura Magnano
- Department of Hematology, Hospital Clínic de Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Jordina Rovira
- Department of Hematology, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Ivan Dlouhy
- Department of Hematology, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Silvia Martín
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Miguel Osuna
- Hematopathology Unit, Department of Pathology, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Sonia Rodríguez
- Department of Radiology, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Marc Simó
- Department of Nuclear Medicine, Instituto Universitario Dexeus, Grupo Quiron Salud, Barcelona, Spain
| | - Magda Pinyol
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Tycho Baumann
- Department of Hematology, Hospital Clínic de Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Silvia Beà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Olga Balagué
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Hematopathology Unit, Department of Pathology, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Julio Delgado
- Department of Hematology, Hospital Clínic de Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Neus Villamor
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Hematopathology Unit, Department of Pathology, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Xavier Setoain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Department of Nuclear Medicine, Hospital Clínic de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBERBBN), Madrid, Spain
| | - Elías Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Hematopathology Unit, Department of Pathology, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Eva Giné
- Department of Hematology, Hospital Clínic de Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Armando López-Guillermo
- Department of Hematology, Hospital Clínic de Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
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14
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Serrat N, Guerrero-Hernández M, Matas-Céspedes A, Yahiaoui A, Valero JG, Nadeu F, Clot G, Di Re M, Corbera-Bellalta M, Magnano L, Rivas-Delgado A, Enjuanes A, Beà S, Cid MC, Campo E, Montero J, Hodson DJ, López-Guillermo A, Colomer D, Tannheimer S, Pérez-Galán P. PI3Kδ inhibition reshapes follicular lymphoma-immune microenvironment cross talk and unleashes the activity of venetoclax. Blood Adv 2020; 4:4217-4231. [PMID: 32898249 PMCID: PMC7479943 DOI: 10.1182/bloodadvances.2020001584] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 07/23/2020] [Indexed: 12/17/2022] Open
Abstract
Despite idelalisib approval in relapsed follicular lymphoma (FL), a complete characterization of the immunomodulatory consequences of phosphatidylinositol 3-kinase δ (PI3Kδ) inhibition, biomarkers of response, and potential combinatorial therapies in FL remain to be established. Using ex vivo cocultures of FL patient biopsies and follicular dendritic cells (FDCs) to mimic the germinal center (n = 42), we uncovered that PI3Kδ inhibition interferes with FDC-induced genes related to angiogenesis, extracellular matrix formation, and transendothelial migration in a subset of FL samples, defining an 18-gene signature fingerprint of idelalisib sensitivity. A common hallmark of idelalisib found in all FL cases was its interference with the CD40/CD40L pathway and induced proliferation, together with the downregulation of proteins crucial for B-T-cell synapses, leading to an inefficient cross talk between FL cells and the supportive T-follicular helper cells (TFH). Moreover, idelalisib downmodulates the chemokine CCL22, hampering the recruitment of TFH and immunosupressive T-regulatory cells to the FL niche, leading to a less supportive and tolerogenic immune microenvironment. Finally, using BH3 profiling, we uncovered that FL-FDC and FL-macrophage cocultures augment tumor addiction to BCL-XL and MCL-1 or BFL-1, respectively, limiting the cytotoxic activity of the BCL-2 inhibitor venetoclax. Idelalisib restored FL dependence on BCL-2 and venetoclax activity. In summary, idelalisib exhibits a patient-dependent activity toward angiogenesis and lymphoma dissemination. In all FL cases, idelalisib exerts a general reshaping of the FL immune microenvironment and restores dependence on BCL-2, predisposing FL to cell death, providing a mechanistic rationale for investigating the combination of PI3Kδ inhibitors and venetoclax in clinical trials.
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Affiliation(s)
- Neus Serrat
- Department of Hematology-Oncology, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Martina Guerrero-Hernández
- Department of Hematology-Oncology, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Alba Matas-Céspedes
- Department of Hematology-Oncology, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red-Oncología, Madrid, Spain
| | - Anella Yahiaoui
- Department of Biomarker Sciences, Gilead Sciences, Inc., Seattle, WA
| | - Juan G Valero
- Department of Hematology-Oncology, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red-Oncología, Madrid, Spain
| | - Ferran Nadeu
- Department of Hematology-Oncology, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red-Oncología, Madrid, Spain
| | - Guillem Clot
- Department of Hematology-Oncology, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red-Oncología, Madrid, Spain
| | - Miriam Di Re
- Department of Haematology, Wellcome Medical Research Council Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Marc Corbera-Bellalta
- Vasculitis Research Unit, Department of Autoimmune Diseases, Clinical Institute of Medicine and Dermatology, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS-CRB CELLEX), Barcelona, Spain
| | - Laura Magnano
- Centro de Investigación Biomédica en Red-Oncología, Madrid, Spain
- Department of Hematology and
| | - Alfredo Rivas-Delgado
- Centro de Investigación Biomédica en Red-Oncología, Madrid, Spain
- Department of Hematology and
| | - Anna Enjuanes
- Department of Hematology-Oncology, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red-Oncología, Madrid, Spain
| | - Silvia Beà
- Department of Hematology-Oncology, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red-Oncología, Madrid, Spain
| | - Maria C Cid
- Vasculitis Research Unit, Department of Autoimmune Diseases, Clinical Institute of Medicine and Dermatology, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS-CRB CELLEX), Barcelona, Spain
| | - Elías Campo
- Department of Hematology-Oncology, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red-Oncología, Madrid, Spain
- Hematopathology Unit, Department of Pathology, Hospital Clínic-IDIBAPS, Barcelona, Spain; and
| | - Joan Montero
- Department of Nanobioengineering, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Daniel J Hodson
- Department of Haematology, Wellcome Medical Research Council Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Armando López-Guillermo
- Centro de Investigación Biomédica en Red-Oncología, Madrid, Spain
- Department of Hematology and
| | - Dolors Colomer
- Department of Hematology-Oncology, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red-Oncología, Madrid, Spain
- Hematopathology Unit, Department of Pathology, Hospital Clínic-IDIBAPS, Barcelona, Spain; and
| | - Stacey Tannheimer
- Department of Biomarker Sciences, Gilead Sciences, Inc., Seattle, WA
| | - Patricia Pérez-Galán
- Department of Hematology-Oncology, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red-Oncología, Madrid, Spain
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15
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Croci GA, Hoster E, Beà S, Clot G, Enjuanes A, Scott DW, Cabeçadas J, Veloza L, Campo E, Clasen-Linde E, Goswami RS, Helgeland L, Pileri S, Rymkiewicz G, Reinke S, Dreyling M, Klapper W. Reproducibility of histologic prognostic parameters for mantle cell lymphoma: cytology, Ki67, p53 and SOX11. Virchows Arch 2020; 477:259-267. [PMID: 31975037 DOI: 10.1007/s00428-020-02750-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/04/2020] [Accepted: 01/09/2020] [Indexed: 01/04/2023]
Abstract
Mantle cell lymphoma (MCL) shows a clinical aggressiveness that varies from patient to patient. Despite major advances in outcomes with current immunochemotherapy, the future development of therapies requires risk stratification to tailor therapy intensity. Within the group of reference pathologists for the ongoing trials of the European MCL Network, we performed a round robin test on a tissue microarray to evaluate the reproducibility in assessing the biomarkers of outcome in MCL. Cytological subtype, Ki67-index and expression of p53 and SOX11 were evaluated on 20 diagnostic tumour samples by eight participating labs independently. We demonstrate that the assessment of the proliferation index by counting the Ki67 positive cells as well as assessment of SOX11 and p53 expression status is reproducible between labs. For the most established prognostic biomarker, Ki67, the intra-class correlation coefficient was very good when assessed as a continuous parameter (0.87). The agreement was lower when the values were analysed in a dichotomized way applying the commonly used cutoff of 30% (kappa = 0.65, complete concordance of all labs in 13/20 (65%)). Cases with discrepant results between labs in the dichotomized analysis showed mean values close to the cutoff of 30%. Centralised scoring and digital image analysis revealed results in line with the scores from individual labs. All cases in our cohort were additionally assessed for gene expression signatures and of TP53 gene alterations. Given the good reproducibility when guidelines of assessment are applied, the biomarker studied in this inter-laboratory test presents potential candidates to be enhanced for risk-stratification in the future clinical trials.
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Affiliation(s)
- Giorgio A Croci
- Hematopathology Section, Institute of Pathology and Lymph Node Registry, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany. .,Pathology Unit, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy. .,UOC di Anatomia Patologica, IRCCS Fondazione Ca' Granda - Ospedale Maggiore Policlinico, Via Francesco Sforza, 35 - 20122, Milano, Italy.
| | - Eva Hoster
- Institute for Medical Information Processing, Biometry and Epidemiology (IBE), Ludwig-Maximilians-Universität Munich, Munich, Germany.,Department of Medicine III, University Hospital of the Ludwig Maximilians University Munich, Munich, Germany
| | - Sílvia Beà
- Institute for Biomedical Research August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Guillem Clot
- Institute for Biomedical Research August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Anna Enjuanes
- Institute for Biomedical Research August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - David W Scott
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, Canada
| | - José Cabeçadas
- Department of Pathology, Instituto Português de Oncologia de Lisboa Francisco Gentil, E.P.E, Lisbon, Portugal
| | - Luis Veloza
- Hematopathology Unit-Laboratory of Pathology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Elias Campo
- Institute for Biomedical Research August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Hematopathology Unit-Laboratory of Pathology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | | | - Rashmi S Goswami
- Sunnybrook Health Sciences Centre, Dept. of Laboratory Medicine and Molecular Diagnostics, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Lars Helgeland
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Stefano Pileri
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan, Italy
| | - Grzegorz Rymkiewicz
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Institute-Oncology Centre, Warsaw, Poland
| | - Sarah Reinke
- Hematopathology Section, Institute of Pathology and Lymph Node Registry, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Martin Dreyling
- Department of Medicine III, University Hospital of the Ludwig Maximilians University Munich, Munich, Germany
| | - Wolfram Klapper
- Hematopathology Section, Institute of Pathology and Lymph Node Registry, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
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16
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Ciavarella S, Vegliante MC, Fabbri M, De Summa S, Melle F, Motta G, De Iuliis V, Opinto G, Enjuanes A, Rega S, Gulino A, Agostinelli C, Scattone A, Tommasi S, Mangia A, Mele F, Simone G, Zito AF, Ingravallo G, Vitolo U, Chiappella A, Tarella C, Gianni AM, Rambaldi A, Zinzani PL, Casadei B, Derenzini E, Loseto G, Pileri A, Tabanelli V, Fiori S, Rivas-Delgado A, López-Guillermo A, Venesio T, Sapino A, Campo E, Tripodo C, Guarini A, Pileri SA. Dissection of DLBCL microenvironment provides a gene expression-based predictor of survival applicable to formalin-fixed paraffin-embedded tissue. Ann Oncol 2019; 30:2015. [PMID: 31539020 PMCID: PMC6938597 DOI: 10.1093/annonc/mdz386] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- S Ciavarella
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - M C Vegliante
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - M Fabbri
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan
| | - S De Summa
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - F Melle
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan
| | - G Motta
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan
| | - V De Iuliis
- Post-graduated Medical School of Clinical Pathology, "Gabriele D'Annunzio", University of Chieti, Chieti
| | - G Opinto
- Functional Biomorphology Laboratory, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - A Enjuanes
- Unitat de Genòmica, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona; CIBERONC, Barcelona, Spain
| | - S Rega
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - A Gulino
- Tumor Immunology Unit, Dipartimento per la Promozione della Salute e Materno Infantile "G. D'Alessandro", University of Palermo, Palermo
| | - C Agostinelli
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), Bologna University School of Medicine, Bologna
| | - A Scattone
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - S Tommasi
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - A Mangia
- Functional Biomorphology Laboratory, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - F Mele
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - G Simone
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - A F Zito
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - G Ingravallo
- Pathology Section, Department of Emergency and Organ Transplantation (DETO), University of Bari "Aldo Moro", Bari
| | - U Vitolo
- Department of Hematology, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Torino
| | - A Chiappella
- Department of Hematology, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Torino
| | - C Tarella
- Onco-Hematology Unit, European Institute of Oncology, IRCCS, Milan
| | - A M Gianni
- Onco-Hematology Unit, European Institute of Oncology, IRCCS, Milan
| | - A Rambaldi
- Department of Hematology and Oncology, Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII, Bergamo; School of Medicine, University of Milan, Milan, Italy
| | - P L Zinzani
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), Bologna University School of Medicine, Bologna
| | - B Casadei
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), Bologna University School of Medicine, Bologna
| | - E Derenzini
- Onco-Hematology Unit, European Institute of Oncology, IRCCS, Milan
| | - G Loseto
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - A Pileri
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), Bologna University School of Medicine, Bologna
| | - V Tabanelli
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan
| | - S Fiori
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan
| | - A Rivas-Delgado
- CIBERONC, Barcelona, Spain; Hematology Department, Hospital Clínic, Barcelona; IDIBAPS, Barcelona, Spain
| | - A López-Guillermo
- CIBERONC, Barcelona, Spain; Hematology Department, Hospital Clínic, Barcelona; IDIBAPS, Barcelona, Spain
| | - T Venesio
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - A Sapino
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy; Department of Medical Sciences, University of Torino, Turin, Italy
| | - E Campo
- CIBERONC, Barcelona, Spain; Haematopathology Unit, Pathology Department, Hospital Clínic, Barcelona; University of Barcelona, Barcelona, Spain
| | - C Tripodo
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - A Guarini
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari
| | - S A Pileri
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan
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17
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Ciavarella S, Vegliante MC, Fabbri M, De Summa S, Melle F, Motta G, De Iuliis V, Opinto G, Enjuanes A, Rega S, Gulino A, Agostinelli C, Scattone A, Tommasi S, Mangia A, Mele F, Simone G, Zito AF, Ingravallo G, Vitolo U, Chiappella A, Tarella C, Gianni AM, Rambaldi A, Zinzani PL, Casadei B, Derenzini E, Loseto G, Pileri A, Tabanelli V, Fiori S, Rivas-Delgado A, López-Guillermo A, Venesio T, Sapino A, Campo E, Tripodo C, Guarini A, Pileri SA. Dissection of DLBCL microenvironment provides a gene expression-based predictor of survival applicable to formalin-fixed paraffin-embedded tissue. Ann Oncol 2019; 29:2363-2370. [PMID: 30307529 PMCID: PMC6311951 DOI: 10.1093/annonc/mdy450] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Gene expression profiling (GEP) studies recognized a prognostic role for tumor microenvironment (TME) in diffuse large B-cell lymphoma (DLBCL), but the routinely adoption of prognostic stromal signatures remains limited. Patients and methods Here, we applied the computational method CIBERSORT to generate a 1028-gene matrix incorporating signatures of 17 immune and stromal cytotypes. Then, we carried out a deconvolution on publicly available GEP data of 482 untreated DLBCLs to reveal associations between clinical outcomes and proportions of putative tumor-infiltrating cell types. Forty-five genes related to peculiar prognostic cytotypes were selected and their expression digitally quantified by NanoString technology on a validation set of 175 formalin-fixed, paraffin-embedded DLBCLs from two randomized trials. Data from an unsupervised clustering analysis were used to build a model of clustering assignment, whose prognostic value was also assessed on an independent cohort of 40 cases. All tissue samples consisted of pretreatment biopsies of advanced-stage DLBCLs treated by comparable R-CHOP/R-CHOP-like regimens. Results In silico analysis demonstrated that higher proportion of myofibroblasts (MFs), dendritic cells, and CD4+ T cells correlated with better outcomes and the expression of genes in our panel is associated with a risk of overall and progression-free survival. In a multivariate Cox model, the microenvironment genes retained high prognostic performance independently of the cell-of-origin (COO), and integration of the two prognosticators (COO + TME) improved survival prediction in both validation set and independent cohort. Moreover, the major contribution of MF-related genes to the panel and Gene Set Enrichment Analysis suggested a strong influence of extracellular matrix determinants in DLBCL biology. Conclusions Our study identified new prognostic categories of DLBCL, providing an easy-to-apply gene panel that powerfully predicts patients’ survival. Moreover, owing to its relationship with specific stromal and immune components, the panel may acquire a predictive relevance in clinical trials exploring new drugs with known impact on TME.
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Affiliation(s)
- S Ciavarella
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - M C Vegliante
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - M Fabbri
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan, Italy
| | - S De Summa
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - F Melle
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan, Italy
| | - G Motta
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan, Italy
| | - V De Iuliis
- Post-graduated Medical School of Clinical Pathology, "Gabriele D'Annunzio", University of Chieti, Chieti, Italy
| | - G Opinto
- Functional Biomorphology Laboratory, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - A Enjuanes
- Unitat de Genòmica, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; CIBERONC, Barcelona, Spain
| | - S Rega
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - A Gulino
- Tumor Immunology Unit, Dipartimento per la Promozione della Salute e Materno Infantile "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - C Agostinelli
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), Bologna University School of Medicine, Bologna, Italy
| | - A Scattone
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - S Tommasi
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - A Mangia
- Functional Biomorphology Laboratory, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - F Mele
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - G Simone
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - A F Zito
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - G Ingravallo
- Pathology Section, Department of Emergency and Organ Transplantation (DETO), University of Bari "Aldo Moro", Bari, Italy
| | - U Vitolo
- Department of Hematology, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Torino, Italy
| | - A Chiappella
- Department of Hematology, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Torino, Italy
| | - C Tarella
- Onco-Hematology Unit, European Institute of Oncology, IRCCS, Milan, Italy
| | - A M Gianni
- Onco-Hematology Unit, European Institute of Oncology, IRCCS, Milan, Italy
| | - A Rambaldi
- Department of Hematology and Oncology, Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy; School of Medicine, University of Milan, Milan, Italy
| | - P L Zinzani
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), Bologna University School of Medicine, Bologna, Italy
| | - B Casadei
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), Bologna University School of Medicine, Bologna, Italy
| | - E Derenzini
- Onco-Hematology Unit, European Institute of Oncology, IRCCS, Milan, Italy
| | - G Loseto
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - A Pileri
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), Bologna University School of Medicine, Bologna, Italy
| | - V Tabanelli
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan, Italy
| | - S Fiori
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan, Italy
| | - A Rivas-Delgado
- CIBERONC, Barcelona, Spain; Hematology Department, Hospital Clínic, Barcelona, Spain; IDIBAPS, Barcelona, Spain
| | - A López-Guillermo
- CIBERONC, Barcelona, Spain; Hematology Department, Hospital Clínic, Barcelona, Spain; IDIBAPS, Barcelona, Spain
| | - T Venesio
- Pathology Department, Candiolo Cancer Institute, Turin, Italy
| | - A Sapino
- Pathology Department, Candiolo Cancer Institute, Turin, Italy
| | - E Campo
- CIBERONC, Barcelona, Spain; Haematopathology Unit, Pathology Department, Hospital Clínic, Barcelona, Spain; University of Barcelona, Barcelona, Spain
| | - C Tripodo
- Pathology Department, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - A Guarini
- Hematology and Cell Therapy Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', Bari, Italy
| | - S A Pileri
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Milan, Italy.
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18
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Rivas-Delgado A, Nadeu F, Enjuanes A, Magnano L, Castrejón de Anta N, Mozas P, Baumann T, Delgado J, Balagué O, Villamor N, Campo E, Giné E, López-Guillermo A. MUTATIONAL LANDSCAPE OF DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) AT DIAGNOSIS AND AT PROGRESSION ASSESSED BY CIRCULATING TUMOR DNA ANALYSIS. Hematol Oncol 2019. [DOI: 10.1002/hon.1_2630] [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: 11/10/2022]
Affiliation(s)
- A. Rivas-Delgado
- Hematology Department; Hospital Clínic de Barcelona; Barcelona Spain
| | - F. Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Hospital Clínic; Barcelona Spain
| | - A. Enjuanes
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Hospital Clínic; Barcelona Spain
| | - L. Magnano
- Hematopathology Unit; Department of Pathology, Hospital Clínic de Barcelona; Barcelona Spain
| | | | - P. Mozas
- Hematology Department; Hospital Clínic de Barcelona; Barcelona Spain
| | - T. Baumann
- Hematology Department; Hospital Clínic de Barcelona; Barcelona Spain
| | - J. Delgado
- Hematology Department; Hospital Clínic de Barcelona; Barcelona Spain
| | - O. Balagué
- Department of Pathology; Hospital Clínic de Barcelona; Barcelona Spain
| | - N. Villamor
- Hematopathology Unit; Department of Pathology, Hospital Clínic de Barcelona; Barcelona Spain
| | - E. Campo
- Department of Pathology; Hospital Clínic de Barcelona; Barcelona Spain
| | - E. Giné
- Hematology Department; Hospital Clínic de Barcelona; Barcelona Spain
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19
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Rivas-Delgado A, Nadeu F, Enjuanes A, Magnano L, Mozas P, Osuna M, Martín S, Baumann T, Castrejón de Anta N, Balagué O, Delgado J, Villamor N, Campo E, Giné E, López-Guillermo A. GENOTYPING PRIMARY MEDIASTINAL B-CELL LYMPHOMA (PMBCL) BY MEANS OF CIRCULATING TUMOR DNA ANALYSIS. Hematol Oncol 2019. [DOI: 10.1002/hon.9_2631] [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]
Affiliation(s)
- A. Rivas-Delgado
- Hematology Department; Hospital Clínic de Barcelona; Barcelona Spain
| | - F. Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Hospital Clínic; Barcelona Spain
| | - A. Enjuanes
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Hospital Clínic; Barcelona Spain
| | - L. Magnano
- Hematopathology Unit; Department of Pathology, Hospital Clínic de Barcelona; Barcelona Spain
| | - P. Mozas
- Hematology Department; Hospital Clínic de Barcelona; Barcelona Spain
| | - M. Osuna
- Hematopathology Unit; Department of Pathology, Hospital Clínic de Barcelona; Barcelona Spain
| | - S. Martín
- Hematopathology Unit; Department of Pathology, Hospital Clínic de Barcelona; Barcelona Spain
| | - T. Baumann
- Hematology Department; Hospital Clínic de Barcelona; Barcelona Spain
| | | | - O. Balagué
- Department of Pathology; Hospital Clínic de Barcelona; Barcelona Spain
| | - J. Delgado
- Hematology Department; Hospital Clínic de Barcelona; Barcelona Spain
| | - N. Villamor
- Hematopathology Unit; Department of Pathology, Hospital Clínic de Barcelona; Barcelona Spain
| | - E. Campo
- Department of Pathology; Hospital Clínic de Barcelona; Barcelona Spain
| | - E. Giné
- Hematology Department; Hospital Clínic de Barcelona; Barcelona Spain
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20
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Albero R, Enjuanes A, Demajo S, Castellano G, Pinyol M, García N, Capdevila C, Clot G, Suárez-Cisneros H, Shimada M, Karube K, López-Guerra M, Colomer D, Beà S, Martin-Subero JI, Campo E, Jares P. Cyclin D1 overexpression induces global transcriptional downregulation in lymphoid neoplasms. J Clin Invest 2018; 128:4132-4147. [PMID: 29990311 DOI: 10.1172/jci96520] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 06/28/2018] [Indexed: 01/05/2023] Open
Abstract
Cyclin D1 is an oncogene frequently overexpressed in human cancers that has a dual function as cell cycle and transcriptional regulator, although the latter is widely unexplored. Here, we investigated the transcriptional role of cyclin D1 in lymphoid tumor cells with cyclin D1 oncogenic overexpression. Cyclin D1 showed widespread binding to the promoters of most actively transcribed genes, and the promoter occupancy positively correlated with the transcriptional output of targeted genes. Despite this association, the overexpression of cyclin D1 in lymphoid cells led to a global transcriptional downmodulation that was proportional to cyclin D1 levels. This cyclin D1-dependent global transcriptional downregulation was associated with a reduced nascent transcription and an accumulation of promoter-proximal paused RNA polymerase II (Pol II) that colocalized with cyclin D1. Concordantly, cyclin D1 overexpression promoted an increase in the Poll II pausing index. This transcriptional impairment seems to be mediated by the interaction of cyclin D1 with the transcription machinery. In addition, cyclin D1 overexpression sensitized cells to transcription inhibitors, revealing a synthetic lethality interaction that was also observed in primary mantle cell lymphoma cases. This finding of global transcriptional dysregulation expands the known functions of oncogenic cyclin D1 and suggests the therapeutic potential of targeting the transcriptional machinery in cyclin D1-overexpressing tumors.
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Affiliation(s)
| | - Anna Enjuanes
- Genomics Unit, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | | | | | - Magda Pinyol
- Genomics Unit, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | | | | | | | - Helena Suárez-Cisneros
- Genomics Unit, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Mariko Shimada
- Hematopathology Unit and Cell Biology, Graduate School of Medicine and Faculty of Medicine, University of the Ryukyus, Nishihara, Japan.,Haematopathology Unit, Department of Anatomic Pathology, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Kennosuke Karube
- Hematopathology Unit and Cell Biology, Graduate School of Medicine and Faculty of Medicine, University of the Ryukyus, Nishihara, Japan.,Haematopathology Unit, Department of Anatomic Pathology, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Mónica López-Guerra
- Lymphoid Neoplasm Program and.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Haematopathology Unit, Department of Anatomic Pathology, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Dolors Colomer
- Lymphoid Neoplasm Program and.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Haematopathology Unit, Department of Anatomic Pathology, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Sílvia Beà
- Lymphoid Neoplasm Program and.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - José Ignacio Martin-Subero
- Lymphoid Neoplasm Program and.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Elías Campo
- Lymphoid Neoplasm Program and.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Haematopathology Unit, Department of Anatomic Pathology, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Pedro Jares
- Lymphoid Neoplasm Program and.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Molecular Biology Core, Hospital Clinic of Barcelona, Barcelona, Spain.,Haematopathology Unit, Department of Anatomic Pathology, Hospital Clínic, University of Barcelona, Barcelona, Spain
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21
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Beekman R, Chapaprieta V, Russiñol N, Vilarrasa-Blasi R, Verdaguer-Dot N, Martens JHA, Duran-Ferrer M, Kulis M, Serra F, Javierre BM, Wingett SW, Clot G, Queirós AC, Castellano G, Blanc J, Gut M, Merkel A, Heath S, Vlasova A, Ullrich S, Palumbo E, Enjuanes A, Martín-García D, Beà S, Pinyol M, Aymerich M, Royo R, Puiggros M, Torrents D, Datta A, Lowy E, Kostadima M, Roller M, Clarke L, Flicek P, Agirre X, Prosper F, Baumann T, Delgado J, López-Guillermo A, Fraser P, Yaspo ML, Guigó R, Siebert R, Martí-Renom MA, Puente XS, López-Otín C, Gut I, Stunnenberg HG, Campo E, Martin-Subero JI. The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia. Nat Med 2018; 24:868-880. [PMID: 29785028 DOI: 10.1038/s41591-018-0028-4] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 03/23/2018] [Indexed: 12/11/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is a frequent hematological neoplasm in which underlying epigenetic alterations are only partially understood. Here, we analyze the reference epigenome of seven primary CLLs and the regulatory chromatin landscape of 107 primary cases in the context of normal B cell differentiation. We identify that the CLL chromatin landscape is largely influenced by distinct dynamics during normal B cell maturation. Beyond this, we define extensive catalogues of regulatory elements de novo reprogrammed in CLL as a whole and in its major clinico-biological subtypes classified by IGHV somatic hypermutation levels. We uncover that IGHV-unmutated CLLs harbor more active and open chromatin than IGHV-mutated cases. Furthermore, we show that de novo active regions in CLL are enriched for NFAT, FOX and TCF/LEF transcription factor family binding sites. Although most genetic alterations are not associated with consistent epigenetic profiles, CLLs with MYD88 mutations and trisomy 12 show distinct chromatin configurations. Furthermore, we observe that non-coding mutations in IGHV-mutated CLLs are enriched in H3K27ac-associated regulatory elements outside accessible chromatin. Overall, this study provides an integrative portrait of the CLL epigenome, identifies extensive networks of altered regulatory elements and sheds light on the relationship between the genetic and epigenetic architecture of the disease.
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Affiliation(s)
- Renée Beekman
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Universitat de Barcelona, Barcelona, Spain
| | - Vicente Chapaprieta
- Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Núria Russiñol
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Roser Vilarrasa-Blasi
- Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Núria Verdaguer-Dot
- Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Joost H A Martens
- Molecular Biology, NCMLS, FNWI, Radboud University, Nijmegen, The Netherlands
| | - Martí Duran-Ferrer
- Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Marta Kulis
- Fundació Clínic per a la Recerca Biomèdica, Barcelona, Spain
| | - François Serra
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Structural Genomics Group, CNAG-CRG, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Biola M Javierre
- Nuclear Dynamics Program, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Steven W Wingett
- Nuclear Dynamics Program, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Guillem Clot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Universitat de Barcelona, Barcelona, Spain
| | - Ana C Queirós
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Julie Blanc
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Marta Gut
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Angelika Merkel
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Simon Heath
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Anna Vlasova
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology and UPF, Barcelona, Spain
| | - Sebastian Ullrich
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology and UPF, Barcelona, Spain
| | - Emilio Palumbo
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology and UPF, Barcelona, Spain
| | - Anna Enjuanes
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Universitat de Barcelona, Barcelona, Spain
| | - David Martín-García
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Universitat de Barcelona, Barcelona, Spain
| | - Sílvia Beà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Universitat de Barcelona, Barcelona, Spain
| | - Magda Pinyol
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Universitat de Barcelona, Barcelona, Spain
| | - Marta Aymerich
- Centro de Investigación Biomédica en Red de Cáncer, Universitat de Barcelona, Barcelona, Spain.,Unitat de Hematología, Hospital Clínic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - Romina Royo
- Programa Conjunto de Biología Computacional, Barcelona Supercomputing Center (BSC), Institut de Recerca Biomèdica (IRB), Spanish National Bioinformatics Institute, Universitat de Barcelona, Barcelona, Spain
| | - Montserrat Puiggros
- Programa Conjunto de Biología Computacional, Barcelona Supercomputing Center (BSC), Institut de Recerca Biomèdica (IRB), Spanish National Bioinformatics Institute, Universitat de Barcelona, Barcelona, Spain
| | - David Torrents
- Programa Conjunto de Biología Computacional, Barcelona Supercomputing Center (BSC), Institut de Recerca Biomèdica (IRB), Spanish National Bioinformatics Institute, Universitat de Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Avik Datta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK
| | - Ernesto Lowy
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK
| | - Myrto Kostadima
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK
| | - Maša Roller
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK
| | - Xabier Agirre
- Centro de Investigación Biomédica en Red de Cáncer, Universitat de Barcelona, Barcelona, Spain.,Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
| | - Felipe Prosper
- Centro de Investigación Biomédica en Red de Cáncer, Universitat de Barcelona, Barcelona, Spain.,Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain.,Clínica Universidad de Navarra, Universidad de Navarra, Pamplona, Spain
| | - Tycho Baumann
- Centro de Investigación Biomédica en Red de Cáncer, Universitat de Barcelona, Barcelona, Spain.,Servicio de Hematología, Hospital Clínic, IDIBAPS, Barcelona, Spain
| | - Julio Delgado
- Centro de Investigación Biomédica en Red de Cáncer, Universitat de Barcelona, Barcelona, Spain.,Servicio de Hematología, Hospital Clínic, IDIBAPS, Barcelona, Spain
| | - Armando López-Guillermo
- Centro de Investigación Biomédica en Red de Cáncer, Universitat de Barcelona, Barcelona, Spain.,Servicio de Hematología, Hospital Clínic, IDIBAPS, Barcelona, Spain
| | - Peter Fraser
- Nuclear Dynamics Program, Babraham Institute, Babraham Research Campus, Cambridge, UK.,Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | | | - Roderic Guigó
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology and UPF, Barcelona, Spain
| | - Reiner Siebert
- Institute of Human Genetics, University of Ulm and University Hospital of Ulm, Ulm, Germany
| | - Marc A Martí-Renom
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Structural Genomics Group, CNAG-CRG, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Xose S Puente
- Centro de Investigación Biomédica en Red de Cáncer, Universitat de Barcelona, Barcelona, Spain.,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Carlos López-Otín
- Centro de Investigación Biomédica en Red de Cáncer, Universitat de Barcelona, Barcelona, Spain.,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Ivo Gut
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Universitat de Barcelona, Barcelona, Spain.,Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain.,Fundació Clínic per a la Recerca Biomèdica, Barcelona, Spain.,Hematopathology Section, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Jose I Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer, Universitat de Barcelona, Barcelona, Spain. .,Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain.
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22
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Nadeu F, Clot G, Delgado J, Martín-García D, Baumann T, Salaverria I, Beà S, Pinyol M, Jares P, Navarro A, Suárez-Cisneros H, Aymerich M, Rozman M, Villamor N, Colomer D, González M, Alcoceba M, Terol MJ, Navarro B, Colado E, Payer ÁR, Puente XS, López-Otín C, López-Guillermo A, Enjuanes A, Campo E. Clinical impact of the subclonal architecture and mutational complexity in chronic lymphocytic leukemia. Leukemia 2018; 32:645-653. [PMID: 28924241 PMCID: PMC5843898 DOI: 10.1038/leu.2017.291] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/07/2017] [Accepted: 09/05/2017] [Indexed: 12/11/2022]
Abstract
Genome studies of chronic lymphocytic leukemia (CLL) have revealed the remarkable subclonal heterogeneity of the tumors, but the clinical implications of this phenomenon are not well known. We assessed the mutational status of 28 CLL driver genes by deep-targeted next-generation sequencing and copy number alterations (CNA) in 406 previously untreated patients and 48 sequential samples. We detected small subclonal mutations (0.6-25% of cells) in nearly all genes (26/28), and they were the sole alteration in 22% of the mutated cases. CNA tended to be acquired early in the evolution of the disease and remained stable, whereas the mutational heterogeneity increased in a subset of tumors. The prognostic impact of different genes was related to the size of the mutated clone. Combining mutations and CNA, we observed that the accumulation of driver alterations (mutational complexity) gradually shortened the time to first treatment independently of the clonal architecture, IGHV status and Binet stage. Conversely, the overall survival was associated with the increasing subclonal diversity of the tumors but it was related to the age of patients, IGHV and TP53 status of the tumors. In conclusion, our study reveals that both the mutational complexity and subclonal diversity influence the evolution of CLL.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor
- Clonal Evolution/genetics
- DNA Copy Number Variations
- Disease Progression
- Female
- Follow-Up Studies
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Male
- Middle Aged
- Mutation/genetics
- Neoplasm Staging
- Prognosis
- Proportional Hazards Models
- Signal Transduction
- Young Adult
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Affiliation(s)
- F Nadeu
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - G Clot
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - J Delgado
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - D Martín-García
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - T Baumann
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - I Salaverria
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - S Beà
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - M Pinyol
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Unitat de Genòmica, IDIBAPS, Barcelona, Spain
| | - P Jares
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - A Navarro
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - M Aymerich
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - M Rozman
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - N Villamor
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - D Colomer
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - M González
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Biología Molecular e Histocompatibilidad, Hospital Universitario, Salamanca, Spain
| | - M Alcoceba
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Biología Molecular e Histocompatibilidad, Hospital Universitario, Salamanca, Spain
| | - M J Terol
- Unidad de Hematología, Hospital Clínico Universitario, Valencia, Spain
| | - B Navarro
- Unidad de Hematología, Hospital Clínico Universitario, Valencia, Spain
| | - E Colado
- Servicio de Hematología y Hemoterapia, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - ÁR Payer
- Servicio de Hematología y Hemoterapia, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - X S Puente
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - C López-Otín
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - A López-Guillermo
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
- Medical School, Universitat de Barcelona, Barcelona, Spain
| | - A Enjuanes
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Unitat de Genòmica, IDIBAPS, Barcelona, Spain
| | - E Campo
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
- Medical School, Universitat de Barcelona, Barcelona, Spain
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23
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Karube K, Enjuanes A, Dlouhy I, Jares P, Martin-Garcia D, Nadeu F, Ordóñez GR, Rovira J, Clot G, Royo C, Navarro A, Gonzalez-Farre B, Vaghefi A, Castellano G, Rubio-Perez C, Tamborero D, Briones J, Salar A, Sancho JM, Mercadal S, Gonzalez-Barca E, Escoda L, Miyoshi H, Ohshima K, Miyawaki K, Kato K, Akashi K, Mozos A, Colomo L, Alcoceba M, Valera A, Carrió A, Costa D, Lopez-Bigas N, Schmitz R, Staudt LM, Salaverria I, López-Guillermo A, Campo E. Integrating genomic alterations in diffuse large B-cell lymphoma identifies new relevant pathways and potential therapeutic targets. Leukemia 2017; 32:675-684. [PMID: 28804123 PMCID: PMC5843901 DOI: 10.1038/leu.2017.251] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [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: 04/19/2017] [Revised: 07/24/2017] [Accepted: 07/27/2017] [Indexed: 02/08/2023]
Abstract
Genome studies of diffuse large B-cell lymphoma (DLBCL) have revealed a large number of somatic mutations and structural alterations. However, the clinical significance of these alterations is still not well defined. In this study, we have integrated the analysis of targeted next-generation sequencing of 106 genes and genomic copy number alterations (CNA) in 150 DLBCL. The clinically significant findings were validated in an independent cohort of 111 patients. Germinal center B-cell and activated B-cell DLBCL had a differential profile of mutations, altered pathogenic pathways and CNA. Mutations in genes of the NOTCH pathway and tumor suppressor genes (TP53/CDKN2A), but not individual genes, conferred an unfavorable prognosis, confirmed in the independent validation cohort. A gene expression profiling analysis showed that tumors with NOTCH pathway mutations had a significant modulation of downstream target genes, emphasizing the relevance of this pathway in DLBCL. An in silico drug discovery analysis recognized 69 (46%) cases carrying at least one genomic alteration considered a potential target of drug response according to early clinical trials or preclinical assays in DLBCL or other lymphomas. In conclusion, this study identifies relevant pathways and mutated genes in DLBCL and recognizes potential targets for new intervention strategies.
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Affiliation(s)
- K Karube
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,Department of Pathology and Cell Biology, Graduate School of Medicine and Faculty of Medicine, University of the Ryukyus, Nishihara, Japan
| | - A Enjuanes
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - I Dlouhy
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - P Jares
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - D Martin-Garcia
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - F Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | | | - J Rovira
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - G Clot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - C Royo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - A Navarro
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - B Gonzalez-Farre
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - A Vaghefi
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - G Castellano
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - C Rubio-Perez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - D Tamborero
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - J Briones
- Servei de Patologia, Hospital de Sant Pau, Barcelona, Spain
| | - A Salar
- Department of Pathology, Hospital del Mar, Universitat Pompeu Fabra, Barcelona, Spain
| | - J M Sancho
- ICO-Hospital Germans Trias i Pujol, Barcelona, Spain
| | - S Mercadal
- ICO-Hospital Duran i Reynals, L'Hospitalet, Barcelona, Spain
| | | | - L Escoda
- Department of Hematology, Hospital Universitari Joan XXIII, Tarragona, Spain
| | - H Miyoshi
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan
| | - K Ohshima
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan
| | - K Miyawaki
- Department of Medicine and Biosystemic Science, Graduate School of Medical Science, Kyushu University, Fukuoka, Japan
| | - K Kato
- Department of Medicine and Biosystemic Science, Graduate School of Medical Science, Kyushu University, Fukuoka, Japan
| | - K Akashi
- Department of Medicine and Biosystemic Science, Graduate School of Medical Science, Kyushu University, Fukuoka, Japan
| | - A Mozos
- Servei de Patologia, Hospital de Sant Pau, Barcelona, Spain
| | - L Colomo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,Department of Pathology, Hospital del Mar, Universitat Pompeu Fabra, Barcelona, Spain
| | - M Alcoceba
- CIBERONC, Madrid, Spain.,Unidad de Biología Molecular/Histocompatibilidad, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - A Valera
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - A Carrió
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - D Costa
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - N Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - R Schmitz
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - L M Staudt
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - I Salaverria
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - A López-Guillermo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - E Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
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24
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Dlouhy I, Karube K, Enjuanes A, Salaverría I, Pérez-Galán P, Jares P, Martín-García D, Nadeu F, Rivas-Delgado A, Rovira J, Gonzalez B, Mozos A, Clot G, Sancho J, Salar A, Mercadal S, Escola L, Briones J, Colomo L, Alcoceba M, Valera A, Campo E, López-Guillermo A. GENE MUTATIONS AND COPY NUMBER ALTERATIONS (CNA) PREDICT FOR EARLY FAILURE IN PATIENTS WITH DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) TREATED WITH R-CHOP. Hematol Oncol 2017. [DOI: 10.1002/hon.2437_82] [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)
- I. Dlouhy
- Hematology; Hospital Clinic Barcelona; Barcelona Spain
| | - K. Karube
- Department of Pathology and Cell Biology, Graduate School of Medicine and Faculty of Medicine; University of the Ryukyus; Nishihara Japan
| | - A. Enjuanes
- Hematology; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Barcelona Spain
| | - I. Salaverría
- Hematology; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Barcelona Spain
| | - P. Pérez-Galán
- Hematology; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Barcelona Spain
| | - P. Jares
- Hematology; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Barcelona Spain
| | - D. Martín-García
- Hematology; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Barcelona Spain
| | - F. Nadeu
- Hematology; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Barcelona Spain
| | | | - J. Rovira
- Hematology; Hospital Clinic Barcelona; Barcelona Spain
| | - B. Gonzalez
- Pathology; Hospital Clinic Barcelona; Barcelona Spain
| | - A. Mozos
- Pathology; Hospital Clinic Barcelona; Barcelona Spain
| | - G. Clot
- Hematology; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Barcelona Spain
| | - J.M. Sancho
- Hematology; ICO-Hospital Germans Trias i Pujol; Barcelona Spain
| | - A. Salar
- Hematology; Hospital del Mar; Barcelona Spain
| | - S. Mercadal
- Hematology; ICO-Hospital Duran i Reynals; Barcelona Spain
| | - L. Escola
- Hematology; Hospital Universitari Joan XXIII; Tarragona Spain
| | - J. Briones
- Hematology; Hospital de Sant Pau; Barcelona Spain
| | - L. Colomo
- Pathology; Hospital del Mar; Barcelona Spain
| | - M. Alcoceba
- Hematology; Hospital Universitario de Salamanca; Salamanca Spain
| | - A. Valera
- Hematology; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Barcelona Spain
| | - E. Campo
- Hematology; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Barcelona Spain
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25
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Queirós AC, Beekman R, Vilarrasa-Blasi R, Duran-Ferrer M, Clot G, Merkel A, Raineri E, Russiñol N, Castellano G, Beà S, Navarro A, Kulis M, Verdaguer-Dot N, Jares P, Enjuanes A, Calasanz MJ, Bergmann A, Vater I, Salaverría I, van de Werken HJG, Wilson WH, Datta A, Flicek P, Royo R, Martens J, Giné E, Lopez-Guillermo A, Stunnenberg HG, Klapper W, Pott C, Heath S, Gut IG, Siebert R, Campo E, Martín-Subero JI. Decoding the DNA Methylome of Mantle Cell Lymphoma in the Light of the Entire B Cell Lineage. Cancer Cell 2016; 30:806-821. [PMID: 27846393 PMCID: PMC5805090 DOI: 10.1016/j.ccell.2016.09.014] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 07/18/2016] [Accepted: 09/19/2016] [Indexed: 01/17/2023]
Abstract
We analyzed the in silico purified DNA methylation signatures of 82 mantle cell lymphomas (MCL) in comparison with cell subpopulations spanning the entire B cell lineage. We identified two MCL subgroups, respectively carrying epigenetic imprints of germinal-center-inexperienced and germinal-center-experienced B cells, and we found that DNA methylation profiles during lymphomagenesis are largely influenced by the methylation dynamics in normal B cells. An integrative epigenomic approach revealed 10,504 differentially methylated regions in regulatory elements marked by H3K27ac in MCL primary cases, including a distant enhancer showing de novo looping to the MCL oncogene SOX11. Finally, we observed that the magnitude of DNA methylation changes per case is highly variable and serves as an independent prognostic factor for MCL outcome.
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Affiliation(s)
- Ana C Queirós
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain
| | - Renée Beekman
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Roser Vilarrasa-Blasi
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain
| | - Martí Duran-Ferrer
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain
| | - Guillem Clot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Angelika Merkel
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Emanuele Raineri
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Nuria Russiñol
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Giancarlo Castellano
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Sílvia Beà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Alba Navarro
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Marta Kulis
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain
| | - Núria Verdaguer-Dot
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Pedro Jares
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Unidad de Genómica, IDIBAPS, Barcelona 08036, Spain
| | | | | | - Anke Bergmann
- Institute of Human Genetics, Christian-Albrechts University, Kiel 24105, Germany; Department of Pediatrics, Christian-Albrechts University & University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Inga Vater
- Institute of Human Genetics, Christian-Albrechts University, Kiel 24105, Germany
| | - Itziar Salaverría
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Harmen J G van de Werken
- Department of Cell Biology, Erasmus MC, Rotterdam 3015 CN, the Netherlands; Cancer Computational Biology Center, Erasmus MC, Rotterdam 3015 CN, the Netherlands; Department of Urology, Erasmus MC, Rotterdam 3015 CN, the Netherlands
| | - Wyndham H Wilson
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Avik Datta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Romina Royo
- Joint Program on Computational Biology, Barcelona Supercomputing Center (BSC) and Institute of Research in Biomedicine (IRB), Barcelona Science Park, Barcelona 08034, Spain
| | - Joost Martens
- Molecular Biology, NCMLS, FNWI, Radboud University, Nijmegen 6500 HB, the Netherlands
| | - Eva Giné
- Servicio de Hematología, Hospital Clínic, IDIBAPS, Barcelona 08036, Spain
| | | | - Hendrik G Stunnenberg
- Molecular Biology, NCMLS, FNWI, Radboud University, Nijmegen 6500 HB, the Netherlands
| | - Wolfram Klapper
- Hematopathology Section and Lymph Node Registry, Christian-Albrecht University, Kiel 24105, Germany
| | - Christiane Pott
- Second Medical Department, University Hospital Schleswig-Holstein, Kiel 24116, Germany
| | - Simon Heath
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts University, Kiel 24105, Germany
| | - Elías Campo
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain; Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Barcelona 08036, Spain
| | - José I Martín-Subero
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain.
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26
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Rovira J, Karube K, Valera A, Colomer D, Enjuanes A, Colomo L, Martínez-Trillos A, Giné E, Dlouhy I, Magnano L, Delgado J, Martínez A, Villamor N, Campo E, López-Guillermo A. MYD88 L265P Mutations, But No Other Variants, Identify a Subpopulation of DLBCL Patients of Activated B-cell Origin, Extranodal Involvement, and Poor Outcome. Clin Cancer Res 2016; 22:2755-64. [PMID: 26792260 DOI: 10.1158/1078-0432.ccr-15-1525] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 01/05/2016] [Indexed: 11/16/2022]
Abstract
PURPOSE Mutations in MYD88 are found in different lymphoproliferative disorders associated with particular biologic characteristics and clinical impact. The aim of this study was to analyze the incidence of MYD88 mutations and its clinical impact in diffuse large B-cell lymphoma (DLBCL). EXPERIMENTAL DESIGN The incidence, clinicobiological features, and outcome of 213 patients (115 M/98 F; median age, 65 years) with DLBCL treated with immunochemotherapy in a single institution according to MYD88 mutational status as assessed by an allele-specific PCR assay were analyzed. The cell of origin (COO) was determined in 129 cases by gene expression. RESULTS MYD88 mutations were found in 47 cases (22%), including L265P in 39 and S219C and M232F in 4 cases, respectively. Patients with MYD88 L265P were older, presenting frequent extranodal involvement, and mostly corresponded to activated B-cell like (ABC) subtype, whereas no preference in COO was observed in patients with other MYD88 mutations. Five-year overall survival (OS) for MYD88 wild-type, MYD88 L265P, and other variants was 62%, 52%, and 75%, respectively (P = 0.05). International Prognostic Index (IPI) (HR, 2.71; P < 0.001) and MYD88 L265P (HR, 1.786; P = 0.023) were independent variables predicting OS in the multivariate analysis. However, MYD88 L265P lost its independent value when COO was included in the model. CONCLUSIONS Our findings indicate that MYD88 L265P mutations, but no other variants, identify a subgroup of DLBCL mainly of ABC origin, with extranodal involvement and poor outcome. Clin Cancer Res; 22(11); 2755-64. ©2016 AACR.
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Affiliation(s)
- Jordina Rovira
- Hematology Department, Hospital Clínic, IDIBAPS, Barcelona, Spain
| | - Kennosuke Karube
- Pathology Department, Hospital Clínic, IDIBAPS, Barcelona, Spain
| | - Alexandra Valera
- Pathology Department, Hospital Clínic, IDIBAPS, Barcelona, Spain
| | - Dolors Colomer
- Pathology Department, Hospital Clínic, IDIBAPS, Barcelona, Spain
| | - Anna Enjuanes
- Genomics Unit, Hospital Clínic, IDIBAPS, Barcelona, Spain
| | - Lluís Colomo
- Pathology Department, Hospital Clínic, IDIBAPS, Barcelona, Spain
| | | | - Eva Giné
- Hematology Department, Hospital Clínic, IDIBAPS, Barcelona, Spain
| | - Ivan Dlouhy
- Hematology Department, Hospital Clínic, IDIBAPS, Barcelona, Spain
| | - Laura Magnano
- Hematology Department, Hospital Clínic, IDIBAPS, Barcelona, Spain
| | - Julio Delgado
- Hematology Department, Hospital Clínic, IDIBAPS, Barcelona, Spain
| | - Antonio Martínez
- Pathology Department, Hospital Clínic, IDIBAPS, Barcelona, Spain
| | - Neus Villamor
- Pathology Department, Hospital Clínic, IDIBAPS, Barcelona, Spain
| | - Elías Campo
- Pathology Department, Hospital Clínic, IDIBAPS, Barcelona, Spain. Universitat Barcelona, Barcelona, Spain
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Corbera-Bellalta M, Planas-Rigol E, Lozano E, Terrades-García N, Alba MA, Prieto-González S, García-Martínez A, Albero R, Enjuanes A, Espígol-Frigolé G, Hernández-Rodríguez J, Roux-Lombard P, Ferlin WG, Dayer JM, Kosco-Vilbois MH, Cid MC. Blocking interferon γ reduces expression of chemokines CXCL9, CXCL10 and CXCL11 and decreases macrophage infiltration in ex vivo cultured arteries from patients with giant cell arteritis. Ann Rheum Dis 2015; 75:1177-86. [DOI: 10.1136/annrheumdis-2015-208371] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 11/06/2015] [Indexed: 01/21/2023]
Abstract
BackgroundInterferon γ (IFNγ) is considered a seminal cytokine in the pathogenesis of giant cell arteritis (GCA), but its functional role has not been investigated. We explored changes in infiltrating cells and biomarkers elicited by blocking IFNγ with a neutralising monoclonal antibody, A6, in temporal arteries from patients with GCA.MethodsTemporal arteries from 34 patients with GCA (positive histology) and 21 controls were cultured on 3D matrix (Matrigel) and exposed to A6 or recombinant IFNγ. Changes in gene/protein expression were measured by qRT-PCR/western blot or immunoassay. Changes in infiltrating cells were assessed by immunohistochemistry/immunofluorescence. Chemotaxis/adhesion assays were performed with temporal artery-derived vascular smooth muscle cells (VSMCs) and peripheral blood mononuclear cells (PBMCs).ResultsBlocking endogenous IFNγ with A6 abrogated STAT-1 phosphorylation in cultured GCA arteries. Furthermore, selective reduction in CXCL9, CXCL10 and CXCL11 chemokine expression was observed along with reduction in infiltrating CD68 macrophages. Adding IFNγ elicited consistent opposite effects. IFNγ induced CXCL9, CXCL10, CXCL11, CCL2 and intracellular adhesion molecule-1 expression by cultured VSMC, resulting in increased PBMC chemotaxis/adhesion. Spontaneous expression of chemokines was higher in VSMC isolated from GCA-involved arteries than in those obtained from controls. Incubation of IFNγ-treated control arteries with PBMC resulted in adhesion/infiltration by CD68 macrophages, which did not occur in untreated arteries.ConclusionsOur ex vivo system suggests that IFNγ may play an important role in the recruitment of macrophages in GCA by inducing production of specific chemokines and adhesion molecules. Vascular wall components (ie, VSMC) are mediators of these functions and may facilitate progression of inflammatory infiltrates through the vessel wall.
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Puente XS, Beà S, Valdés-Mas R, Villamor N, Gutiérrez-Abril J, Martín-Subero JI, Munar M, Rubio-Pérez C, Jares P, Aymerich M, Baumann T, Beekman R, Belver L, Carrio A, Castellano G, Clot G, Colado E, Colomer D, Costa D, Delgado J, Enjuanes A, Estivill X, Ferrando AA, Gelpí JL, González B, González S, González M, Gut M, Hernández-Rivas JM, López-Guerra M, Martín-García D, Navarro A, Nicolás P, Orozco M, Payer ÁR, Pinyol M, Pisano DG, Puente DA, Queirós AC, Quesada V, Romeo-Casabona CM, Royo C, Royo R, Rozman M, Russiñol N, Salaverría I, Stamatopoulos K, Stunnenberg HG, Tamborero D, Terol MJ, Valencia A, López-Bigas N, Torrents D, Gut I, López-Guillermo A, López-Otín C, Campo E. Non-coding recurrent mutations in chronic lymphocytic leukaemia. Nature 2015. [DOI: 10.1038/nature14666] [Citation(s) in RCA: 625] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Enjuanes A, Albero R, Clot G, Navarro A, Beà S, Pinyol M, Martín-Subero JI, Klapper W, Staudt LM, Jaffe ES, Rimsza L, Braziel RM, Delabie J, Cook JR, Tubbs RR, Gascoyne R, Connors JM, Weisenburger DD, Greiner TC, Chan WC, López-Guillermo A, Rosenwald A, Ott G, Campo E, Jares P. Genome-wide methylation analyses identify a subset of mantle cell lymphoma with a high number of methylated CpGs and aggressive clinicopathological features. Int J Cancer 2013; 133:2852-63. [PMID: 23754783 DOI: 10.1002/ijc.28321] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 04/23/2013] [Indexed: 01/02/2023]
Abstract
Mantle cell lymphoma (MCL) is a B-cell neoplasm with an aggressive clinical behavior characterized by the t(11;14)(q13;q32) and cyclin D1 overexpression. To clarify the potential contribution of altered DNA methylation in the development and/or progression of MCL, we performed genome-wide methylation profiling of a large cohort of primary MCL tumors (n = 132), MCL cell lines (n = 6) and normal lymphoid tissue samples (n = 31), using the Infinium HumanMethylation27 BeadChip. DNA methylation was compared to gene expression, chromosomal alterations and clinicopathological parameters. Primary MCL displayed a heterogeneous methylation pattern dominated by DNA hypomethylation when compared to normal lymphoid samples. A total of 454 hypermethylated and 875 hypomethylated genes were identified as differentially methylated in at least 10% of primary MCL. Annotation analysis of hypermethylated genes recognized WNT pathway inhibitors and several tumor suppressor genes as frequently methylated, and a substantial fraction of these genes (22%) showed a significant downregulation of their transcriptional levels. Furthermore, we identified a subset of tumors with extensive CpG methylation that had an increased proliferation signature, higher number of chromosomal alterations and poor prognosis. Our results suggest that a subset of MCL displays a dysregulation of DNA methylation characterized by the accumulation of CpG hypermethylation highly associated with increased proliferation that may influence the clinical behavior of the tumors.
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Affiliation(s)
- Anna Enjuanes
- Genomics Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
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Enjuanes A, Benavente Y, Hernández-Rodríguez J, Queralt C, Yagüe J, Jares P, de Sanjosé S, Campo E, Cid MC. Association of NOS2 and potential effect of VEGF, IL6, CCL2 and IL1RN polymorphisms and haplotypes on susceptibility to GCA--a simultaneous study of 130 potentially functional SNPs in 14 candidate genes. Rheumatology (Oxford) 2012; 51:841-51. [PMID: 22258388 DOI: 10.1093/rheumatology/ker429] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVE Frequent genetic variants may be associated with GCA. Existing studies have analysed a limited number of candidate genes and genetic variants. To expand this information, we performed a case-control study genotyping 130 single nucleotide polymorphisms (SNPs) in 82 biopsy-proven GCA patients and 166 healthy controls from the Spanish population. METHODS SNPs in coding and regulatory gene regions of 14 candidate genes (CCL2, CCR7, IL10, IL12A, IL1A, IL1B, IL1RN, IL6, IL8, INFG, LTA, NOS2, TNF and VEGF) were explored using the Illumina Bead Array System. Multivariate methods based on logistic regression were used for statistical analysis. RESULTS Nine SNPs located in five genes had significant association with GCA risk (P < 0.05). These SNPs were located in the NOS2 (rs2779251), VEGF (rs1885657, rs2010963, rs699946 and rs699947), IL1RN (rs17207494), IL6 (rs7805828 and rs1546766) and CCL2 (rs1860190) genes. The strongest associations were seen for rs2779251, rs1885657 and rs2010963 (P = 2.3 × 10(-5), P = 0.0078 and P = 0.0097, respectively). The presence of the minor allele of NOS2 variant rs2779251 had a protective effect on the risk for GCA [odds ratio (OR) = 0.27, 95% CI 0.14, 0.52]. Risk alleles for three of the four SNPs in the VEGF gene (rs2010963, rs699946 and rs699947) were associated in homozygosis with increased risk (OR = 4.22, 95% CI 1.38, 12.87; OR = 9.04, 95% CI 1.58, 51.81; and OR = 2.38, 95% CI 1.05, 5.38, respectively), whereas a minor allele for the other SNP (rs1885657) had a protective effect (OR = 0.46, 95% CI 0.26, 0.84). CONCLUSION Common genetic variants in NOS2, VEGF, IL6, ILRN1 and CCL2 genes are associated with GCA, indicating a polygenic influence on disease susceptibility.
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Affiliation(s)
- Anna Enjuanes
- Department of Systemic Autoimmune Diseases, Hospital Clínic, Villarroel 170, 08036-Barcelona, Spain
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Ruiz-Gaspà S, Martinez-Ferrer A, Guañabens N, Dubreuil M, Peris P, Enjuanes A, Martinez de Osaba MJ, Alvarez L, Monegal A, Combalia A, Parés A. Effects of bilirubin and sera from jaundiced patients on osteoblasts: contribution to the development of osteoporosis in liver diseases. Hepatology 2011; 54:2104-13. [PMID: 21837749 DOI: 10.1002/hep.24605] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
UNLABELLED Low bone formation is considered to be the main feature in osteoporosis associated with cholestatic and end-stage liver diseases, although the consequences of retained substances in chronic cholestasis on bone cells have scarcely been studied. Therefore, we analyzed the effects of bilirubin and serum from jaundiced patients on viability, differentiation, mineralization, and gene expression in the cells involved in bone formation. The experiments were performed in human primary osteoblasts and SAOS-2 human osteosarcoma cells. Unconjugated bilirubin or serum from jaundiced patients resulted in a dose-dependent decrease in osteoblast viability. Concentrations of bilirubin or jaundiced serum without effects on cell survival significantly diminished osteoblast differentiation. Mineralization was significantly reduced by exposure to 50 μM bilirubin at all time points (from -32% to -55%) and jaundiced sera resulted in a significant decrease on cell mineralization as well. Furthermore, bilirubin down-regulated RUNX2 (runt-related transcription factor 2) gene expression, a basic osteogenic factor involved in osteoblast differentiation, and serum from jaundiced patients significantly up-regulated the RANKL/OPG (receptor activator of nuclear factor-κB ligand/osteoprotegerin) gene expression ratio, a system closely involved in osteoblast-induced osteoclastogenesis. CONCLUSION Besides decreased cell viability, unconjugated bilirubin and serum from jaundiced patients led to defective consequences on osteoblasts. Moreover, jaundiced serum up-regulates the system involved in osteoblast-induced osteoclastogenesis. These results support the deleterious consequences of increased bilirubin in advanced chronic cholestasis and in end-stage liver diseases, resulting in disturbed bone formation related to osteoblast dysfunction.
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Affiliation(s)
- Silvia Ruiz-Gaspà
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBERehd), Institut d’Investigacions Biome`diques August Pi i Sunyer, University of Barcelona, Barcelona, Spain.
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Martín-Guerrero I, Enjuanes A, Richter J, Ammerpohl O, Colomer D, Ardanaz M, Marco F, Salas A, Campo E, Siebert R, García-Orad A. A putative "hepitype" in the ATM gene associated with chronic lymphocytic leukemia risk. Genes Chromosomes Cancer 2011; 50:887-95. [PMID: 21910157 DOI: 10.1002/gcc.20912] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 07/05/2011] [Indexed: 12/12/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) cells are characterized by several chromosomal lesions. Some of these aberrations imply chromosome breaks as a result of unrepaired double strand breaks (DSBs) in the DNA. The ATM (ataxia telangiectasia-mutated) protein is the principal integrator of cellular responses to DSBs. ATM deletion is also an adverse prognostic factor in CLL. Taking this into account, we evaluated if genetic and/or epigenetic variation in the ATM gene may modulate the individual susceptibility to develop CLL. Our case-control association study was performed in a large Spanish population of 1,503 individuals, including 742 patients with CLL and 761 controls. We identified one haplotype within the ATM gene that confers an increased risk of CLL development (OR = 1.33; 95% CI: 1.10-1.60). Two polymorphisms of this ATM haplotype eliminated one CpG site each in Introns 15 and 61, causing changes in DNA methylation pattern. These data provide the first evidence for the existence of a putative "hepitype" in the ATM gene associated with CLL risk.
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Affiliation(s)
- Idoia Martín-Guerrero
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Bizkaia, Spain
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Puente XS, Pinyol M, Quesada V, Conde L, Ordóñez GR, Villamor N, Escaramis G, Jares P, Beà S, González-Díaz M, Bassaganyas L, Baumann T, Juan M, López-Guerra M, Colomer D, Tubío JMC, López C, Navarro A, Tornador C, Aymerich M, Rozman M, Hernández JM, Puente DA, Freije JMP, Velasco G, Gutiérrez-Fernández A, Costa D, Carrió A, Guijarro S, Enjuanes A, Hernández L, Yagüe J, Nicolás P, Romeo-Casabona CM, Himmelbauer H, Castillo E, Dohm JC, de Sanjosé S, Piris MA, de Alava E, San Miguel J, Royo R, Gelpí JL, Torrents D, Orozco M, Pisano DG, Valencia A, Guigó R, Bayés M, Heath S, Gut M, Klatt P, Marshall J, Raine K, Stebbings LA, Futreal PA, Stratton MR, Campbell PJ, Gut I, López-Guillermo A, Estivill X, Montserrat E, López-Otín C, Campo E. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 2011; 475:101-5. [PMID: 21642962 PMCID: PMC3322590 DOI: 10.1038/nature10113] [Citation(s) in RCA: 1159] [Impact Index Per Article: 89.2] [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: 11/16/2010] [Accepted: 04/06/2011] [Indexed: 02/06/2023]
Abstract
Chronic lymphocytic leukaemia (CLL), the most frequent leukaemia in adults in Western countries, is a heterogeneous disease with variable clinical presentation and evolution. Two major molecular subtypes can be distinguished, characterized respectively by a high or low number of somatic hypermutations in the variable region of immunoglobulin genes. The molecular changes leading to the pathogenesis of the disease are still poorly understood. Here we performed whole-genome sequencing of four cases of CLL and identified 46 somatic mutations that potentially affect gene function. Further analysis of these mutations in 363 patients with CLL identified four genes that are recurrently mutated: notch 1 (NOTCH1), exportin 1 (XPO1), myeloid differentiation primary response gene 88 (MYD88) and kelch-like 6 (KLHL6). Mutations in MYD88 and KLHL6 are predominant in cases of CLL with mutated immunoglobulin genes, whereas NOTCH1 and XPO1 mutations are mainly detected in patients with unmutated immunoglobulins. The patterns of somatic mutation, supported by functional and clinical analyses, strongly indicate that the recurrent NOTCH1, MYD88 and XPO1 mutations are oncogenic changes that contribute to the clinical evolution of the disease. To our knowledge, this is the first comprehensive analysis of CLL combining whole-genome sequencing with clinical characteristics and clinical outcomes. It highlights the usefulness of this approach for the identification of clinically relevant mutations in cancer.
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Affiliation(s)
- Xose S Puente
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, 33006 Oviedo, Spain
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Enjuanes A, Fernàndez V, Hernández L, Navarro A, Beà S, Pinyol M, López-Guillermo A, Rosenwald A, Ott G, Campo E, Jares P. Identification of methylated genes associated with aggressive clinicopathological features in mantle cell lymphoma. PLoS One 2011; 6:e19736. [PMID: 21603610 PMCID: PMC3095614 DOI: 10.1371/journal.pone.0019736] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 04/05/2011] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Mantle cell lymphoma (MCL) is genetically characterized by the t(11;14)(q13;q32) translocation and a high number of secondary chromosomal alterations. The contribution of DNA methylation to MCL lymphomagenesis is not well known. We sought to identify epigenetically silenced genes in these tumours that might have clinical relevance. METHODOLOGY/PRINCIPAL FINDINGS To identify potential methylated genes in MCL we initially investigated seven MCL cell lines treated with epigenetic drugs and gene expression microarray profiling. The methylation status of selected candidate genes was validated by a quantitative assay and subsequently analyzed in a series of primary MCL (n = 38). After pharmacological reversion we identified 252 potentially methylated genes. The methylation analysis of a subset of these genes (n = 25) in the MCL cell lines and normal B lymphocytes confirmed that 80% of them were methylated in the cell lines but not in normal lymphocytes. The subsequent analysis in primary MCL identified five genes (SOX9, HOXA9, AHR, NR2F2, and ROBO1) frequently methylated in these tumours. The gene methylation events tended to occur in the same primary neoplasms and correlated with higher proliferation, increased number of chromosomal abnormalities, and shorter survival of the patients. CONCLUSIONS We have identified a set of genes whose methylation degree and gene expression levels correlate with aggressive clinicopathological features of MCL. Our findings also suggest that a subset of MCL might show a CpG island methylator phenotype (CIMP) that may influence the behaviour of the tumours.
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Affiliation(s)
- Anna Enjuanes
- Hematopathology Section, Department of Anatomic Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Verònica Fernàndez
- Hematopathology Section, Department of Anatomic Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Luis Hernández
- Hematopathology Section, Department of Anatomic Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Alba Navarro
- Hematopathology Section, Department of Anatomic Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Sílvia Beà
- Hematopathology Section, Department of Anatomic Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Magda Pinyol
- Genomics Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | | | | | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, and Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Elías Campo
- Hematopathology Section, Department of Anatomic Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Pedro Jares
- Hematopathology Section, Department of Anatomic Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
- Genomics Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
- * E-mail:
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Crowther-Swanepoel D, Mansouri M, Enjuanes A, Vega A, Smedby KE, Ruiz-Ponte C, Jurlander J, Juliusson G, Montserrat E, Catovsky D, Campo E, Carracedo A, Rosenquist R, Houlston RS. Verification that common variation at 2q37.1, 6p25.3, 11q24.1, 15q23, and 19q13.32 influences chronic lymphocytic leukaemia risk. Br J Haematol 2010; 150:473-9. [PMID: 20553269 DOI: 10.1111/j.1365-2141.2010.08270.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A recent genome wide association study of chronic lymphocytic leukaemia (CLL) provided evidence that common variation at 2q13 (rs17483466), 2q37.1 (rs13397985), 6p25.3 (rs872071), 11q24.1 (rs735665), 15q23 (rs7176508) and 19q13.32 (rs11083846) affects CLL risk. To verify and further explore the relationship between these variants and CLL risk we genotyped case-control datasets from Spain and Sweden (824 cases, 850 controls). Combined data provided statistically significant support for an association between genotypes at rs13397985, rs872071, rs735665, rs7176508 and rs11083846 and CLL risk. CLL risk increased with increasing numbers of risk alleles (P(trend) = 1.40 x 10(-15)), consistent with a polygenic model of disease susceptibility. These data validate the relationship between common variation and risk of CLL.
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Enjuanes A, Ruiz-Gaspà S, Peris P, Ozalla D, Alvarez L, Combalia A, Martínez de Osaba MJ, Monegal A, Pares A, Guañabens N. The effect of the alendronate on OPG/RANKL system in differentiated primary human osteoblasts. Endocrine 2010; 37:322-8. [PMID: 20960270 DOI: 10.1007/s12020-009-9306-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Accepted: 12/21/2009] [Indexed: 01/06/2023]
Abstract
Alendronate is a well-established treatment for osteoporosis and suppresses bone resorption by a direct effect on osteoclasts and their precursors. The effect of alendronate on osteoclasts is produced, at least in part, by the receptor activator of nuclear factor kappaB ligand (RANKL) and the osteoprotegerin (OPG) synthesized by the osteoblasts. This study analyzes the effect of alendronate in cell viability, alkaline phosphatase (ALP) activity and RANKL and OPG expression in primary human osteoblasts (hOB). Alendronate at concentrations lower than 10⁻⁵ M did not have a toxic effect on hOB in vitro and did not modify the ALP activity at least for 72 h. Alendronate did not change OPG expression in basal, 10% fetal bovine serum (FBS), and vitamin D-treated cultures. Similar results were observed at the protein level. Unexpectedly, alendronate at 10⁻⁷ and 10⁻⁵ M concentrations increased the RANKL expression with the presence of vitamin D in differentiated hOB, and this induction of RANKL mRNA levels by alendronate was dose-dependent. However, this effect was not observed in basal and 10% FBS culture conditions. Thus, we conclude that alendronate does not affect the ALP activity and OPG gene expression in differentiated hOB, but may increase RANKL gene expression induced by vitamin D.
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Affiliation(s)
- Anna Enjuanes
- Metabolic Bone Diseases Unit, Department of Rheumatology, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain.
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37
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Enjuanes A, Ruiz-Gaspà S, Peris P, Ozalla D, Álvarez L, Combalia A, Martínez de Osaba MJ, Monegal A, Pares A, Guañabens N. The effect of the alendronate on OPG/RANKL system in differentiated primary human osteoblasts. Endocrine 2010; 37:180-6. [PMID: 20963568 DOI: 10.1007/s12020-009-9285-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Accepted: 11/10/2009] [Indexed: 01/06/2023]
Abstract
Alendronate is a well-established treatment for osteoporosis and suppresses bone resorption by a direct effect on osteoclasts and their precursors. The effect of alendronate on osteoclasts is produced, at least in part, by the receptor activator of nuclear factor kappaB ligand (RANKL) and the osteoprotegerin (OPG) synthesized by the osteoblasts. This study analyzes the effect of alendronate in cell viability, phosphatase alkaline (ALP) activity and RANKL, and OPG expression in primary human osteoblasts (hOB). Alendronate at concentrations lower than 10(-5) M did not have a toxic effect on hOB in vitro and did not modify the ALP activity at least for 72 h. Alendronate did not change OPG expression in basal, 10% FBS, and vitamin D-treated cultures. Similar results were observed at the protein level. Unexpectedly, alendronate at 10(-7) and 10(-5) M concentrations increased the RANKL expression with the presence of vitamin D in differentiated hOB and this induction of RANKL mRNA levels by alendronate was dose-dependent. However, this effect was not observed in basal and 10% FBS culture conditions. Thus, we conclude that alendronate does not affect the ALP activity and OPG gene expression in differentiated hOB, but may increase RANKL gene expression induced by vitamin D.
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Affiliation(s)
- Anna Enjuanes
- Metabolic Bone Diseases Unit, Department of Rheumatology, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain.
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Crowther-Swanepoel D, Broderick P, Di Bernardo MC, Dobbins SE, Torres M, Mansouri M, Ruiz-Ponte C, Enjuanes A, Rosenquist R, Carracedo A, Jurlander J, Campo E, Juliusson G, Montserrat E, Smedby KE, Dyer MJS, Matutes E, Dearden C, Sunter NJ, Hall AG, Mainou-Fowler T, Jackson GH, Summerfield G, Harris RJ, Pettitt AR, Allsup DJ, Bailey JR, Pratt G, Pepper C, Fegan C, Parker A, Oscier D, Allan JM, Catovsky D, Houlston RS. Common variants at 2q37.3, 8q24.21, 15q21.3 and 16q24.1 influence chronic lymphocytic leukemia risk. Nat Genet 2010; 42:132-6. [PMID: 20062064 PMCID: PMC5321238 DOI: 10.1038/ng.510] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Accepted: 11/20/2009] [Indexed: 12/20/2022]
Abstract
To identify new risk variants for chronic lymphocytic leukemia (CLL), we conducted a genome-wide association study of 299,983 tagging SNPs, with validation in four additional series totaling 2,503 cases and 5,789 controls. We identified four new risk loci for CLL at 2q37.3 (rs757978, FARP2; odds ratio (OR) = 1.39; P = 2.11 x 10(-9)), 8q24.21 (rs2456449; OR = 1.26; P = 7.84 x 10(-10)), 15q21.3 (rs7169431; OR = 1.36; P = 4.74 x 10(-7)) and 16q24.1 (rs305061; OR = 1.22; P = 3.60 x 10(-7)). We also found evidence for risk loci at 15q25.2 (rs783540, CPEB1; OR = 1.18; P = 3.67 x 10(-6)) and 18q21.1 (rs1036935; OR = 1.22; P = 2.28 x 10(-6)). These data provide further evidence for genetic susceptibility to this B-cell hematological malignancy.
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Ruiz-Gaspà S, Guañabens N, Enjuanes A, Peris P, Martinez-Ferrer A, de Osaba MJM, Gonzalez B, Alvarez L, Monegal A, Combalia A, Parés A. Lithocholic acid downregulates vitamin D effects in human osteoblasts. Eur J Clin Invest 2010; 40:25-34. [PMID: 20055894 DOI: 10.1111/j.1365-2362.2009.02230.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Osteoporosis is a common complication in chronic cholestasis. It has been proposed that retained substances such as bile acids may produce a damaging effect on bone cells. This study analyses the effects of lithocholic acid (LCA) on cell survival and vitamin D metabolism in human osteoblasts (hOB). MATERIALS AND METHODS Human osteoblasts cultures were performed with or without foetal bovine serum (FBS) or human albumin (HA) at different LCA concentrations and times with or without vitamin D. RESULTS Lithocholic acid at concentrations higher than 10(-5 )M decreased cell survival. This effect was partially prevented by the presence of FBS or HA. Vitamin D stimulated CYP24A, BGLAP and TNFSF11 expression in hOB and these effects were modified by nontoxic LCA concentrations. LCA significantly decreased vitamin D stimulation of CYP24A, BGLAP and TNFSF11 gene expression at 72%, 79% and 56% (respectively). LCA alone has an agonistic effect, as has vitamin D, thus partially increasing CYP24A and BGLAP expression, but with no changes on TNFRSF11B expression. Equivalent effects of the LCA were observed by performing gene reporter assays using MG-63 cells transfected with constructs containing CYP24A1 promoter regions. CONCLUSIONS Lithocholic acid decreases the stimulatory effect of vitamin D on CYP24A, BGLAP and TNFSF11 expression in hOB. This effect is produced through vitamin D response elements (VDREs), located in the promoter regions of these genes, suggesting that LCA acts as a mild analogous of vitamin D, interacting with the vitamin D receptor. These results may explain the potential deleterious effects of retained bile acids on hOB.
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Affiliation(s)
- S Ruiz-Gaspà
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain.
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Martin-Guerrero I, Enjuanes A, Bosch F, Villamor N, Jares P, Richter J, Ammerpohl O, Siebert R, Campo E, Garcia-Orad A. 9217 DNA reparation genes in genetic and epigenetic susceptibility to Chronic Lymphocytic Leukaemia. EJC Suppl 2009. [DOI: 10.1016/s1359-6349(09)71908-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Guañabens N, Enjuanes A, Alvarez L, Peris P, Caballería L, Jesús Martínez de Osaba M, Cerdá D, Monegal A, Pons F, Parés A. High osteoprotegerin serum levels in primary biliary cirrhosis are associated with disease severity but not with the mRNA gene expression in liver tissue. J Bone Miner Metab 2009; 27:347-54. [PMID: 19229472 DOI: 10.1007/s00774-009-0042-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Accepted: 07/30/2008] [Indexed: 01/03/2023]
Abstract
The influence of osteoprotegerin and RANKL as regulators of osteoclastogenesis and bone remodeling in liver disease and in the development of osteoporosis in primary biliary cirrhosis (PBC) is uncertain. Therefore, 68 women with PBC and 20 healthy females were studied by assessing circulating osteoprotegerin and RANKL. Bone mineral density and markers of bone turnover were measured as well. Osteoprotegerin-mRNA expression was also assessed in liver tissue from 16 patients and 5 controls. Osteoprotegerin was higher in PBC than in controls (5.4 +/- 0.2 vs. 2.9 +/- 0.2 pM/l, P < 0.0001), whilst RANKL was lower in patients than in controls (0.39 +/- 0.06 vs. 1.40 +/- 0.16 pM/l, P < 0.0001). Osteoprotegerin was more elevated in patients with more advanced disease, as defined by bilirubin above 1.2 mg/dl (6.6 +/- 0.6 vs. 5.2 +/- 0.2 pM/l, P = 0.02) or by Mayo over 4 (5.9 +/- 0.3 vs. 4.8 +/- 0.2 pM/l, P = 0.02). Osteoprotegerin and RANKL were unrelated with osteoporosis, and no associations were found with markers of bone remodeling, except for RANKL, which was particularly decreased in patients with low osteocalcin. This marker of bone formation was also higher in patients with elevated circulating osteoprotegerin. Liver osteoprotegerin gene expression was similar in patients and controls, and no correlation was found between liver osteoprotegerin-mRNA and patients' respective circulating levels. In conclusion, osteoprotegerin and RANKL are abnormal in patients with PBC, regardless of osteoporosis. The elevated circulating osteoprotegerin is associated with the severity of disease, but not with gene expression in the liver.
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Affiliation(s)
- Núria Guañabens
- Metabolic Bone Diseases Unit, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, IDIBAPS, University of Barcelona, Barcelona, Spain.
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Enjuanes A, Benavente Y, Bosch F, Martin-Guerrero I, Colomer D, Perez-Alvarez S, Reina O, Ardanaz MT, Jares P, Garcia-Orad A, Pujana MA, Montserrat E, de Sanjose S, Campo E. Genetic Variants in Apoptosis and Immunoregulation-Related Genes Are Associated with Risk of Chronic Lymphocytic Leukemia. Cancer Res 2008; 68:10178-86. [DOI: 10.1158/0008-5472.can-08-2221] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Bustamante M, Nogués X, Enjuanes A, Elosua R, García-Giralt N, Pérez-Edo L, Cáceres E, Carreras R, Mellibovsky L, Balcells S, Díez-Pérez A, Grinberg D. COL1A1, ESR1, VDR and TGFB1 polymorphisms and haplotypes in relation to BMD in Spanish postmenopausal women. Osteoporos Int 2007; 18:235-43. [PMID: 17021946 DOI: 10.1007/s00198-006-0225-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Accepted: 08/28/2006] [Indexed: 12/29/2022]
Abstract
INTRODUCTION AND HYPOTHESIS Genetic studies of osteoporosis have focused on analysing single polymorphisms in individual genes - with inconclusive results. An alternative approach may involve haplotypes and gene-gene interactions. The aim of the study was to test the association between the COL1A1, ESR1, VDR and TGFB1 polymorphisms or haplotypes and bone mineral density (BMD) in Spanish postmenopausal women. METHODS Sixteen polymorphisms were analysed in 719 postmenopausal women. ANOVA, ANCOVA and Xi2 tests were used to perform the statistical analysis. RESULTS COL1A1 -1997G > T (p=0.04) and TGFB1 Leu10Pro (p=0.02) were found to be associated with adjusted lumbar spine (LS) BMD. Interactions were observed between: the COL1A1 -1997 G/T and Sp1 polymorphisms (p < 0.01 for LS BMD) and the COL1A1 -1663 indelT and VDR ApaI polymorphisms (p < 0.01 for femoral neck (FN) BMD). The COL1A1 GDs and ESR1 LPX haplotypes were associated with FN BMD (p=0.03 and p=0.03). CONCLUSIONS Polymorphisms at COL1A1 and TGFB1 and haplotypes at COL1A1 and ESR1 were found to be associated with BMD in a cohort of postmenopausal Spanish women. Moreover, COL1A1 polymorphisms showed significant interactions among them and with the VDR 3' polymorphisms.
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Affiliation(s)
- M Bustamante
- Department of Genetics, Universitat de Barcelona, Barcelona, Spain
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Supervía A, Enjuanes A, Vila J, Mellibovsky L, Nogués X, Díez-Pérez A. [Effect of tobacco smoking on leptin serum levels and its relationship with steroid hormones and bone mineral density]. Med Clin (Barc) 2007; 127:645-7. [PMID: 17169280 DOI: 10.1157/13094819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
BACKGROUND AND OBJECTIVE Leptin is an hormone resulting from the obesity gene. Their actions could be important in the pathogenesis of the osteoporosis. The aim of this study is to analyse the influence of tobacco on serum leptin levels, and its relationship with bone mineral density (BMD) and steroid hormones. SUBJECTS AND METHOD A group of healthy volunteers were recruited and classified as smokers or non-smokers. A subgroup of smokers ceased smoking during one month. Serum leptin and steroids hormones levels were analysed, and a baseline BMD was measured. In the abstinent group the analysis was repeated at the end of the study. RESULTS Fifty-nine healthy volunteers were included (22 of which were smokers). Fifteen smokers remained abstinent for a month. Both groups were similar except in age, being smokers older. Male smokers had lower lumbar BMD (p = 0.017). After adjusting by age, serum leptin levels were higher in smokers than in non-smokers, with statistical differences in women (p = 0.049). Abstinence increased leptin levels, though not reaching statistical significance. An inverse correlation between leptin levels and androstendione in men (r = -0.622; p = 0.001), and a positive correlation with testosterone in women (r = 0.405; p = 0.019) were found. After adjusting by body mass index, only the correlation of leptin levels with androstendione persisted. CONCLUSIONS Leptin negatively correlate with sex hormones in young men and is influenced by smoking in young women. Thus, the hormone could be relevant for bone mass regulation in smoker persons.
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Affiliation(s)
- August Supervía
- Servicio de Medicina Interna y Enfermedades Infecciosas, URFOA-IMIM, Hospital del Mar, Universitat Autònoma de Barcelona, Barcelona, España.
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Ruiz-Gaspa S, Nogues X, Enjuanes A, Monllau JC, Blanch J, Carreras R, Mellibovsky L, Grinberg D, Balcells S, Díez-Perez A, Pedro-Botet J. Simvastatin and atorvastatin enhance gene expression of collagen type 1 and osteocalcin in primary human osteoblasts and MG-63 cultures. J Cell Biochem 2007; 101:1430-8. [PMID: 17252541 DOI: 10.1002/jcb.21259] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To clarify the mechanism of the stimulatory effect of statins on bone formation, we have assessed the effect of simvastatin and atorvastatin on osteoblast activity by analysing cell proliferation, as well as collagen, osteocalcin, and bone morphogenetic protein-2 (BMP2) gene expression in primary human osteoblast (hOB) and MG-63 cell line cultures. Explants of bone from patients without any metabolic disease under orthopedic hip procedures were used to obtain hOB. Cell cultures were established, synchronized, and different concentrations of simvastatin or atorvastatin were added (10(-9) M, 10(-8) M, 10(-7) M, 10(-6) M) during the experiment. Cell proliferation was analyzed after 24 h. Collagen polypeptide alpha1 type 1 (COL1A1) gene expression, osteocalcin, and BMP2 expression levels were quantified by real-time PCR after 24 h incubation with statins. There was a statistically significant decrease in cell proliferation related to simvastatin or atorvastatin addition at all concentrations in primary hOB compared with those not treated. A significant increase in COL1A1, osteocalcin, and BMP2 gene expression was detected when hOB cultures were treated with simvastatin or atorvastatin at different concentrations. Similar but less significant effects were found on MG-63 cells. After statin treatment we observed both an arrest of proliferation in hOB cells and an increase in collagen, osteocalcin, and BMP2 gene expression, consistent with a stimulatory effect towards mature osteoblast differentiation. These findings support the bone-forming effect of statins, probably through the BMP2 pathway.
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Uitterlinden AG, Ralston SH, Brandi ML, Carey AH, Grinberg D, Langdahl BL, Lips P, Lorenc R, Obermayer-Pietsch B, Reeve J, Reid DM, Amedei A, Amidei A, Bassiti A, Bustamante M, Husted LB, Diez-Perez A, Dobnig H, Dunning AM, Enjuanes A, Fahrleitner-Pammer A, Fang Y, Karczmarewicz E, Kruk M, van Leeuwen JPTM, Mavilia C, van Meurs JBJ, Mangion J, McGuigan FEA, Pols HAP, Renner W, Rivadeneira F, van Schoor NM, Scollen S, Sherlock RE, Ioannidis JPA. The association between common vitamin D receptor gene variations and osteoporosis: a participant-level meta-analysis. Ann Intern Med 2006; 145:255-64. [PMID: 16908916 DOI: 10.7326/0003-4819-145-4-200608150-00005] [Citation(s) in RCA: 184] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Polymorphisms of the vitamin D receptor (VDR) gene have been implicated in the genetic regulation of bone mineral density (BMD). However, the clinical impact of these variants remains unclear. OBJECTIVE To evaluate the relation between VDR polymorphisms, BMD, and fractures. DESIGN Prospective multicenter large-scale association study. SETTING The Genetic Markers for Osteoporosis consortium, involving 9 European research teams. PARTICIPANTS 26,242 participants (18,405 women). MEASUREMENTS Cdx2 promoter, FokI, BsmI, ApaI, and TaqI polymorphisms; BMD at the femoral neck and the lumbar spine by dual x-ray absorptiometry; and fractures. RESULTS Comparisons of BMD at the lumbar spine and femoral neck showed nonsignificant differences less than 0.011 g/cm2 for any genotype with or without adjustments. A total of 6067 participants reported a history of fracture, and 2088 had vertebral fractures. For all VDR alleles, odds ratios for fractures were very close to 1.00 (range, 0.98 to 1.02) and collectively the 95% CIs ranged from 0.94 (lowest) to 1.07 (highest). For vertebral fractures, we observed a 9% (95% CI, 0% to 18%; P = 0.039) risk reduction for the Cdx2 A-allele (13% risk reduction in a dominant model). LIMITATIONS The authors analyzed only selected VDR polymorphisms. Heterogeneity was detected in some analyses and may reflect some differences in collection of fracture data across cohorts. Not all fractures were related to osteoporosis. CONCLUSIONS The FokI, BsmI, ApaI, and TaqI VDR polymorphisms are not associated with BMD or with fractures, but the Cdx2 polymorphism may be associated with risk for vertebral fractures.
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Supervía A, Nogués X, Enjuanes A, Vila J, Mellibovsky L, Serrano S, Aubía J, Díez-Pérez A. Effect of smoking and smoking cessation on bone mass, bone remodeling, vitamin D, PTH and sex hormones. J Musculoskelet Neuronal Interact 2006; 6:234-41. [PMID: 17142943] [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] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
OBJECTIVE To assess the effect of smoking and smoking cessation on bone density, bone remodeling markers, sex hormones, and vitamin D-PTH axis in healthy young subjects. MATERIALS AND METHODS We studied 74 healthy people (31 men, 43 women; mean age 32.2 (7) years) divided into 52 never smokers and 22 smokers, 15 of which stopped smoking for one month. RESULTS Male smokers compared with never smokers showed lower BMD (0.971 (0.11) g/cm(2) vs. 1.069 (0.09) g/cm(2), P=0.042); higher plasma estrone levels (32.37 (10.13) pg/mL vs. 20.91 (5.46) pg/mL, P=0.001); and lower serum iPTH levels (16.2 (3.5) pg/mL vs. 28.8 (2.0) pg/mL, P=0.008). In women, BMD values were similar in smokers than in never smokers, but 25-hydroxyvitamin D levels were lower in smokers (31.9 (15.1) ng/mL vs. 16.8 (9.9) ng/mL, P=0.002). After adjusting by age and coffee consumption, female smokers had higher urinary-NTX levels than never smokers. After smoking cessation, statistically significant decreases of 25-hydroxyvitamin D and SHBG plasma levels were observed in men and women, respectively. CONCLUSIONS Tobacco increases bone resorption and affects bone mass by some alterations in sex hormone metabolism, but also importantly by alterations on the vitamin D-PTH axis.
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Enjuanes A, Garcia-Giralt N, Supervía A, Nogués X, Ruiz-Gaspà S, Bustamante M, Mellibovsky L, Grinberg D, Balcells S, Díez-Pérez A. A new SNP in a negative regulatory region of the CYP19A1 gene is associated with lumbar spine BMD in postmenopausal women. Bone 2006; 38:738-43. [PMID: 16344016 DOI: 10.1016/j.bone.2005.10.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Revised: 09/28/2005] [Accepted: 10/11/2005] [Indexed: 10/25/2022]
Abstract
Osteoporosis is a common disease of bone possessing a strong genetic component. Cytochrome P450 aromatase, which is encoded by the CYP19A1 gene, converts androgens to estradiol. Considerable evidence suggests that extragonadal estrogens play an important role in determining bone mineral density (BMD) in postmenopausal women, and, among them, those synthesized in bone cells may also be important for the determination of bone phenotype. Therefore, CYP19A1 is an excellent candidate gene for osteoporosis. Since a region upstream of exon I.3, including exon I.6, was identified as containing repressor elements of promoter pII, we conducted a search for SNPs in this region of CYP19A1. Two SNPs [Aro1(rs4775936) and Aro2] located in exon I.6 and promoter I.6, respectively, were identified and their association with BMD analyzed in a cohort of 256 Spanish postmenopausal women. Aro1(rs4775936), but not Aro2, was associated with lumbar spine BMD (P = 0.029). Homozygotes AA (16% of the women) exhibited significantly higher lumbar spine BMD, compared with GG or GA individuals. Therefore, this study describes the Aro1 polymorphism which lies within a regulatory region and which may be a functional polymorphism, partially responsible for the bone phenotype it is associated with.
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Affiliation(s)
- Anna Enjuanes
- URFOA-IMIM, Hospital del Mar, Universitat Autònoma de Barcelona, C/Passeig Maritim 25, E-08003 Barcelona, Spain.
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Enjuanes A, Garcia-Giralt N, Supervía A, Nogués X, Ruiz-Gaspà S, Bustamante M, Mellibovsky L, Grinberg D, Balcells S, Díez-Pérez A. Functional analysis of the I.3, I.6, pII and I.4 promoters of CYP19 (aromatase) gene in human osteoblasts and their role in vitamin D and dexamethasone stimulation. Eur J Endocrinol 2005; 153:981-8. [PMID: 16322405 DOI: 10.1530/eje.1.02032] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Current evidence suggests that extragonadal estrogens play an important role in bone metabolism. Estrogen biosynthesis is catalyzed by P450aromatase, encoded by the CYP19 gene. The aims of this paper were to study CYP19 gene expression in human osteoblasts under several hormone and cytokine treatments and to define promoter regions involved in this regulation. METHODS CYP19 transcript levels were measured from primary human osteoblasts and MG-63 cells by real-time PCR in basal conditions, and in response to seven different hormones and cytokines. Four promoters of CYP19 gene were cloned upstream of the luciferase gene and transfected into MG-63 cells. The effect of vitamin D and dexamethasone in these promoter activities was evaluated. RESULTS Vitamin D and dexamethasone were potent stimulators of CYP19 transcription, while testosterone and 17beta-estradiol stimulated moderately. Promoter pII proved the most potent in driving transient luciferase expression. Promoter I.4 displayed moderate activity, while promoters I.3 and I.6 were weak. A region upstream of exon I.3, including exon I.6, was identified as containing repressor elements of promoter pII. Promoter I.3 activity was modulated by repressors located within exon I.3, while an enhancer of promoter I.4 was detected within exon I.4. In the absence of fetal calf serum, dexamethasone stimulation was observed on promoters I.3 and I.4, while vitamin D stimulation acted only on promoter I.3. CONCLUSIONS Four regulatory regions of promoters pII, I.3 and I.4 are relevant to CYP19 expression in human osteoblasts. Vitamin D and dexamethasone modulate transcription through these regions.
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Affiliation(s)
- Anna Enjuanes
- URFOA-IMIM, Hospital del Mar, Universitat Autònoma de Barcelona, E-08003 Barcelona, Spain.
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García-Giralt N, Enjuanes A, Bustamante M, Mellibovsky L, Nogués X, Carreras R, Díez-Pérez A, Grinberg D, Balcells S. In vitro functional assay of alleles and haplotypes of two COL1A1-promoter SNPs. Bone 2005; 36:902-8. [PMID: 15814304 DOI: 10.1016/j.bone.2004.12.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2004] [Revised: 11/15/2004] [Accepted: 12/01/2004] [Indexed: 10/25/2022]
Abstract
Osteoporosis is a common disease with a strong genetic component. We previously described two polymorphic sites in the COL1A1 gene promoter, -1997 G/T and -1663indelT, which have been associated with bone mineral density (BMD), a surrogate trait for osteoporosis. Here, we explore the molecular mechanisms underlying this association by performing transient transfections in MG-63 cells of constructs bearing different COL1A1 promoter regions, containing different alleles or haplotypes of the polymorphic sites. These promoter regions drove the transcription of a luciferase reporter gene. The main differences in transcriptional activity relied on an inhibitory region localized to the -1284 to -254 interval. Regarding the polymorphisms, reproducible differences were observed between the alleles of each of them: the G allele at -1997 showed a higher transcriptional activity than the T allele, as did the 7T allele of -1663 as compared with 8T. Accordingly, the T-8T haplotype was the weakest transcriber. A functional interaction was found between the -1997 and -1663 polymorphisms, in that the difference in transcriptional activity between the 7T and 8T alleles was dependent on the allele at -1997. This different transcriptional activity of the two -1663indelT alleles correlated with different binding capacities of the corresponding oligonucleotides to osteoblast nuclear proteins. Supershift assays allowed us to identify one of these proteins as the architectural transcription factor Nmp4/CIZ, a protein known to be an inhibitor of BMP/Smad signalling.
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Affiliation(s)
- Natàlia García-Giralt
- Department of Genetics, Universitat de Barcelona, Av. Diagonal 645, E-08028 Barcelona, Spain
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