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Alcalá S, Villarino L, Ruiz-Cañas L, Couceiro JR, Martínez-Calvo M, Palencia-Campos A, Navarro D, Cabezas-Sainz P, Rodriguez-Arabaolaza I, Cordero-Barreal A, Trilla-Fuertes L, Rubiolo JA, Batres-Ramos S, Vallespinos M, González-Páramos C, Rodríguez J, Gámez-Pozo A, Vara JÁF, Fernández SF, Berlinches AB, Moreno-Mata N, Redondo AMT, Carrato A, Hermann PC, Sánchez L, Torrente S, Fernández-Moreno MÁ, Mascareñas JL, Sainz B. Targeting cancer stem cell OXPHOS with tailored ruthenium complexes as a new anti-cancer strategy. J Exp Clin Cancer Res 2024; 43:33. [PMID: 38281027 PMCID: PMC10821268 DOI: 10.1186/s13046-023-02931-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/11/2023] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND Previous studies by our group have shown that oxidative phosphorylation (OXPHOS) is the main pathway by which pancreatic cancer stem cells (CSCs) meet their energetic requirements; therefore, OXPHOS represents an Achille's heel of these highly tumorigenic cells. Unfortunately, therapies that target OXPHOS in CSCs are lacking. METHODS The safety and anti-CSC activity of a ruthenium complex featuring bipyridine and terpyridine ligands and one coordination labile position (Ru1) were evaluated across primary pancreatic cancer cultures and in vivo, using 8 patient-derived xenografts (PDXs). RNAseq analysis followed by mitochondria-specific molecular assays were used to determine the mechanism of action. RESULTS We show that Ru1 is capable of inhibiting CSC OXPHOS function in vitro, and more importantly, it presents excellent anti-cancer activity, with low toxicity, across a large panel of human pancreatic PDXs, as well as in colorectal cancer and osteosarcoma PDXs. Mechanistic studies suggest that this activity stems from Ru1 binding to the D-loop region of the mitochondrial DNA of CSCs, inhibiting OXPHOS complex-associated transcription, leading to reduced mitochondrial oxygen consumption, membrane potential, and ATP production, all of which are necessary for CSCs, which heavily depend on mitochondrial respiration. CONCLUSIONS Overall, the coordination complex Ru1 represents not only an exciting new anti-cancer agent, but also a molecular tool to dissect the role of OXPHOS in CSCs. Results indicating that the compound is safe, non-toxic and highly effective in vivo are extremely exciting, and have allowed us to uncover unprecedented mechanistic possibilities to fight different cancer types based on targeting CSC OXPHOS.
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Affiliation(s)
- Sonia Alcalá
- Department of Biochemistry, Autónoma University of Madrid, School of Medicine and Department of Cancer, Instituto de Investigaciones Biomédicas (IIBm) Sols-Morreale (CSIC-UAM), Madrid, Spain
- Biomarkers and Personalized Approach to Cancer (BIOPAC) Group, Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Lara Villarino
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Laura Ruiz-Cañas
- Department of Biochemistry, Autónoma University of Madrid, School of Medicine and Department of Cancer, Instituto de Investigaciones Biomédicas (IIBm) Sols-Morreale (CSIC-UAM), Madrid, Spain
- Biomarkers and Personalized Approach to Cancer (BIOPAC) Group, Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - José R Couceiro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Miguel Martínez-Calvo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Adrián Palencia-Campos
- Department of Biochemistry, Autónoma University of Madrid, School of Medicine and Department of Cancer, Instituto de Investigaciones Biomédicas (IIBm) Sols-Morreale (CSIC-UAM), Madrid, Spain
- Biomarkers and Personalized Approach to Cancer (BIOPAC) Group, Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Diego Navarro
- Department of Biochemistry, Autónoma University of Madrid, School of Medicine and Department of Cancer, Instituto de Investigaciones Biomédicas (IIBm) Sols-Morreale (CSIC-UAM), Madrid, Spain
- Biomarkers and Personalized Approach to Cancer (BIOPAC) Group, Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Pablo Cabezas-Sainz
- Department of Zoology, Genetics and Physical Anthropology, Veterinary Faculty, USC, Lugo, Spain
| | - Iker Rodriguez-Arabaolaza
- Department of Biochemistry, Autónoma University of Madrid, School of Medicine and Department of Cancer, Instituto de Investigaciones Biomédicas (IIBm) Sols-Morreale (CSIC-UAM), Madrid, Spain
- Facultad de Ciencia y Técnología, Universidad del País Vasco, 48940, Leioa (Bizkaia), Spain
| | - Alfonso Cordero-Barreal
- Department of Biochemistry, Autónoma University of Madrid, School of Medicine and Department of Cancer, Instituto de Investigaciones Biomédicas (IIBm) Sols-Morreale (CSIC-UAM), Madrid, Spain
- Biomarkers and Personalized Approach to Cancer (BIOPAC) Group, Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Lucia Trilla-Fuertes
- Molecular Oncology and Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Instituto de Investigación Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
- Biomedica Molecular Medicine SL, Madrid, Spain
| | - Juan A Rubiolo
- Department of Zoology, Genetics and Physical Anthropology, Veterinary Faculty, USC, Lugo, Spain
| | - Sandra Batres-Ramos
- Department of Biochemistry, Autónoma University of Madrid, School of Medicine and Department of Cancer, Instituto de Investigaciones Biomédicas (IIBm) Sols-Morreale (CSIC-UAM), Madrid, Spain
- Biomarkers and Personalized Approach to Cancer (BIOPAC) Group, Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Mireia Vallespinos
- Department of Biochemistry, Autónoma University of Madrid, School of Medicine and Department of Cancer, Instituto de Investigaciones Biomédicas (IIBm) Sols-Morreale (CSIC-UAM), Madrid, Spain
- Biomarkers and Personalized Approach to Cancer (BIOPAC) Group, Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Cristina González-Páramos
- Department of Biochemistry, Autónoma University of Madrid, School of Medicine and Department of Cancer, Instituto de Investigaciones Biomédicas (IIBm) Sols-Morreale (CSIC-UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid, Spain
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Jéssica Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Angelo Gámez-Pozo
- Molecular Oncology and Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Instituto de Investigación Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
- Biomedica Molecular Medicine SL, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Molecular Oncology and Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Instituto de Investigación Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
- Centro de Investigación Biomédica en Red, Área Cáncer, CIBERONC, ISCIII, Madrid, Spain
| | - Sara Fra Fernández
- Servicio de Cirugía Torácica, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Amparo Benito Berlinches
- Biomarkers and Personalized Approach to Cancer (BIOPAC) Group, Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Servicio de Anatomía Patológica, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Nicolás Moreno-Mata
- Servicio de Cirugía Torácica, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | | | - Alfredo Carrato
- Biomarkers and Personalized Approach to Cancer (BIOPAC) Group, Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Centro de Investigación Biomédica en Red, Área Cáncer, CIBERONC, ISCIII, Madrid, Spain
- Pancreatic Cancer Europe (PCE) Chairperson, Brussels, Belgium
| | | | - Laura Sánchez
- Department of Zoology, Genetics and Physical Anthropology, Veterinary Faculty, USC, Lugo, Spain
| | - Susana Torrente
- Valuation, Transfer and Entrepreneurship Area, USC, Santiago de Compostela, Spain
| | - Miguel Ángel Fernández-Moreno
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid, Spain
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
- Department of Biochemistry, Autónoma University of Madrid, School of Medicine and Department of Rare Diseases, Instituto de Investigaciones Biomédicas (IIBm) Sols-Morreale (CSIC-UAM), Madrid, Spain
| | - José L Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain.
| | - Bruno Sainz
- Department of Biochemistry, Autónoma University of Madrid, School of Medicine and Department of Cancer, Instituto de Investigaciones Biomédicas (IIBm) Sols-Morreale (CSIC-UAM), Madrid, Spain.
- Biomarkers and Personalized Approach to Cancer (BIOPAC) Group, Area 3 Cancer, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.
- Centro de Investigación Biomédica en Red, Área Cáncer, CIBERONC, ISCIII, Madrid, Spain.
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Trilla-Fuertes L, Gámez-Pozo A, Prado-Vázquez G, López-Vacas R, Soriano V, Garicano F, Lecumberri MJ, Rodríguez de la Borbolla M, Majem M, Pérez-Ruiz E, González-Cao M, Oramas J, Magdaleno A, Fra J, Martín-Carnicero A, Corral M, Puértolas T, Ramos-Ruiz R, Dittmann A, Nanni P, Fresno Vara JÁ, Espinosa E. Multi-omics Characterization of Response to PD-1 Inhibitors in Advanced Melanoma. Cancers (Basel) 2023; 15:4407. [PMID: 37686682 PMCID: PMC10486782 DOI: 10.3390/cancers15174407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
Immunotherapy improves the survival of patients with advanced melanoma, 40% of whom become long-term responders. However, not all patients respond to immunotherapy. Further knowledge of the processes involved in the response and resistance to immunotherapy is still needed. In this study, clinical paraffin samples from fifty-two advanced melanoma patients treated with anti-PD-1 inhibitors were assessed via high-throughput proteomics and RNA-seq. The obtained proteomics and transcriptomics data were analyzed using multi-omics network analyses based on probabilistic graphical models to identify those biological processes involved in the response to immunotherapy. Additionally, proteins related to overall survival were studied. The activity of the node formed by the proteins involved in protein processing in the endoplasmic reticulum and antigen presentation machinery was higher in responders compared to non-responders; the activity of the immune and inflammatory response node was also higher in those with complete or partial responses. A predictor for overall survival based on two proteins (AMBP and PDSM5) was defined. In summary, the response to anti-PD-1 therapy in advanced melanoma is related to protein processing in the endoplasmic reticulum, and also to genes involved in the immune and inflammatory responses. Finally, a two-protein predictor can define survival in advanced disease. The molecular characterization of the mechanisms involved in the response and resistance to immunotherapy in melanoma leads the way to establishing therapeutic alternatives for patients who will not respond to this treatment.
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Affiliation(s)
- Lucía Trilla-Fuertes
- Molecular Oncology Laboratory, Hospital Universitario La Paz-IdiPAZ, 28046 Madrid, Spain; (L.T.-F.); (A.G.-P.); (G.P.-V.); (R.L.-V.); (J.Á.F.V.)
| | - Angelo Gámez-Pozo
- Molecular Oncology Laboratory, Hospital Universitario La Paz-IdiPAZ, 28046 Madrid, Spain; (L.T.-F.); (A.G.-P.); (G.P.-V.); (R.L.-V.); (J.Á.F.V.)
- Biomedica Molecular Medicine SL, 28049 Madrid, Spain
| | - Guillermo Prado-Vázquez
- Molecular Oncology Laboratory, Hospital Universitario La Paz-IdiPAZ, 28046 Madrid, Spain; (L.T.-F.); (A.G.-P.); (G.P.-V.); (R.L.-V.); (J.Á.F.V.)
- Biomedica Molecular Medicine SL, 28049 Madrid, Spain
| | - Rocío López-Vacas
- Molecular Oncology Laboratory, Hospital Universitario La Paz-IdiPAZ, 28046 Madrid, Spain; (L.T.-F.); (A.G.-P.); (G.P.-V.); (R.L.-V.); (J.Á.F.V.)
| | - Virtudes Soriano
- Instituto Valenciano de Oncología, 46009 Valencia, Spain;
- Spanish Melanoma Group (GEM), 08024 Barcelona, Spain; (F.G.); (M.J.L.); (M.R.d.l.B.); (M.M.); (E.P.-R.); (M.G.-C.); (J.O.); (A.M.); (J.F.); (M.C.); (T.P.)
| | - Fernando Garicano
- Spanish Melanoma Group (GEM), 08024 Barcelona, Spain; (F.G.); (M.J.L.); (M.R.d.l.B.); (M.M.); (E.P.-R.); (M.G.-C.); (J.O.); (A.M.); (J.F.); (M.C.); (T.P.)
- Hospital de Galdakao, 48960 Galdakao, Spain
| | - M. José Lecumberri
- Spanish Melanoma Group (GEM), 08024 Barcelona, Spain; (F.G.); (M.J.L.); (M.R.d.l.B.); (M.M.); (E.P.-R.); (M.G.-C.); (J.O.); (A.M.); (J.F.); (M.C.); (T.P.)
- Complejo Hospitalario de Navarra, 31008 Pamplona, Spain
| | - María Rodríguez de la Borbolla
- Spanish Melanoma Group (GEM), 08024 Barcelona, Spain; (F.G.); (M.J.L.); (M.R.d.l.B.); (M.M.); (E.P.-R.); (M.G.-C.); (J.O.); (A.M.); (J.F.); (M.C.); (T.P.)
- Hospital de Valme, 41014 Sevilla, Spain
| | - Margarita Majem
- Spanish Melanoma Group (GEM), 08024 Barcelona, Spain; (F.G.); (M.J.L.); (M.R.d.l.B.); (M.M.); (E.P.-R.); (M.G.-C.); (J.O.); (A.M.); (J.F.); (M.C.); (T.P.)
- Hospital de la Santa Creu i Sant Pau, 08001 Barcelona, Spain
| | - Elisabeth Pérez-Ruiz
- Spanish Melanoma Group (GEM), 08024 Barcelona, Spain; (F.G.); (M.J.L.); (M.R.d.l.B.); (M.M.); (E.P.-R.); (M.G.-C.); (J.O.); (A.M.); (J.F.); (M.C.); (T.P.)
- Unidad de Gestión Clínica Intercentros (UGCI) de Oncología Médica, Hospitales Universitarios Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospitales Universitarios Regional y Virgen de la Victoria, 29010 Málaga, Spain
| | - María González-Cao
- Spanish Melanoma Group (GEM), 08024 Barcelona, Spain; (F.G.); (M.J.L.); (M.R.d.l.B.); (M.M.); (E.P.-R.); (M.G.-C.); (J.O.); (A.M.); (J.F.); (M.C.); (T.P.)
- Hospital Quirón Dexeus, 08028 Barcelona, Spain
| | - Juana Oramas
- Spanish Melanoma Group (GEM), 08024 Barcelona, Spain; (F.G.); (M.J.L.); (M.R.d.l.B.); (M.M.); (E.P.-R.); (M.G.-C.); (J.O.); (A.M.); (J.F.); (M.C.); (T.P.)
- Hospital Universitario de Canarias-San Cristóbal de la Laguna, 38320 Tenerife, Spain
| | - Alejandra Magdaleno
- Spanish Melanoma Group (GEM), 08024 Barcelona, Spain; (F.G.); (M.J.L.); (M.R.d.l.B.); (M.M.); (E.P.-R.); (M.G.-C.); (J.O.); (A.M.); (J.F.); (M.C.); (T.P.)
- Hospital Universitario de Elche y Vega Baja, 03203 Alicante, Spain
| | - Joaquín Fra
- Spanish Melanoma Group (GEM), 08024 Barcelona, Spain; (F.G.); (M.J.L.); (M.R.d.l.B.); (M.M.); (E.P.-R.); (M.G.-C.); (J.O.); (A.M.); (J.F.); (M.C.); (T.P.)
- Hospital Universitario Río Hortega, 47012 Valladolid, Spain
| | - Alfonso Martín-Carnicero
- Spanish Melanoma Group (GEM), 08024 Barcelona, Spain; (F.G.); (M.J.L.); (M.R.d.l.B.); (M.M.); (E.P.-R.); (M.G.-C.); (J.O.); (A.M.); (J.F.); (M.C.); (T.P.)
- Hospital San Pedro, 27347 Logroño, Spain
| | - Mónica Corral
- Spanish Melanoma Group (GEM), 08024 Barcelona, Spain; (F.G.); (M.J.L.); (M.R.d.l.B.); (M.M.); (E.P.-R.); (M.G.-C.); (J.O.); (A.M.); (J.F.); (M.C.); (T.P.)
- Hospital Clínico Lozano Blesa, 50009 Zaragoza, Spain
| | - Teresa Puértolas
- Spanish Melanoma Group (GEM), 08024 Barcelona, Spain; (F.G.); (M.J.L.); (M.R.d.l.B.); (M.M.); (E.P.-R.); (M.G.-C.); (J.O.); (A.M.); (J.F.); (M.C.); (T.P.)
- Hospital Universitario Miguel Servet, 50009 Zaragoza, Spain
| | | | - Antje Dittmann
- Functional Genomics Center Zurich, University/ETH Zurich, 8092 Zurich, Switzerland; (A.D.); (P.N.)
| | - Paolo Nanni
- Functional Genomics Center Zurich, University/ETH Zurich, 8092 Zurich, Switzerland; (A.D.); (P.N.)
| | - Juan Ángel Fresno Vara
- Molecular Oncology Laboratory, Hospital Universitario La Paz-IdiPAZ, 28046 Madrid, Spain; (L.T.-F.); (A.G.-P.); (G.P.-V.); (R.L.-V.); (J.Á.F.V.)
- Biomedica Molecular Medicine SL, 28049 Madrid, Spain
- CIBERONC, ISCIII, 28222 Madrid, Spain
| | - Enrique Espinosa
- Spanish Melanoma Group (GEM), 08024 Barcelona, Spain; (F.G.); (M.J.L.); (M.R.d.l.B.); (M.M.); (E.P.-R.); (M.G.-C.); (J.O.); (A.M.); (J.F.); (M.C.); (T.P.)
- CIBERONC, ISCIII, 28222 Madrid, Spain
- Medical Oncology Service, Hospital Universitario La Paz, 28046 Madrid, Spain
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Zapater-Moros A, Díaz-Beltrán L, Gámez-Pozo A, Trilla-Fuertes L, Lumbreras-Herrera MI, López-Camacho E, González-Olmedo C, Espinosa E, Zamora P, Sánchez-Rovira P, Fresno Vara JÁ. Metabolomics unravels subtype-specific characteristics related to neoadjuvant therapy response in breast cancer patients. Metabolomics 2023; 19:60. [PMID: 37344702 DOI: 10.1007/s11306-023-02024-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/09/2023] [Indexed: 06/23/2023]
Abstract
INTRODUCTION Breast cancer is the most diagnosed tumor and the leading cause of cancer death in women worldwide. Metabolomics allows the quantification of the entire set of metabolites in blood samples, making it possible to study differential metabolomics patterns related to neoadjuvant treatment in the breast cancer neoadjuvant setting. OBJECTIVES Characterizing metabolic differences in breast cancer blood samples according to their response to neoadjuvant treatment. METHODS One hundred and three plasma samples of breast cancer patients, before receiving neoadjuvant treatment, were analyzed through UPLC-MS/MS metabolomics. Then, metabolomics data were analyzed using probabilistic graphical models and biostatistics methods. RESULTS Metabolomics data allowed the identification of differences between groups according to response to neoadjuvant treatment. These differences were specific to each breast cancer subtype. Patients with HER2+ tumors showed differences in metabolites related to amino acids and carbohydrates pathways between the two pathological response groups. However, patients with triple-negative tumors showed differences in metabolites related to the long-chain fatty acids pathway. Patients with Luminal B tumors showed differences in metabolites related to acylcarnitine pathways. CONCLUSIONS It is possible to identify differential metabolomics patterns between complete and partial responses to neoadjuvant therapy, being this metabolomic profile specific for each breast cancer subtype.
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Affiliation(s)
- Andrea Zapater-Moros
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
- Biomedica Molecular Medicine SL, C/Faraday 7, 28049, Madrid, Spain
- Biomedical Research Networking Center On Oncology-CIBERONC, ISCIII, Av. Monforte de Lemos 5, 28029, Madrid, Spain
| | - Leticia Díaz-Beltrán
- Systems Biology Unit, Department of Experimental Biology, University of Jaén, Campus Las Lagunillas s/n, 23071, Jaén, Spain
- Medical Oncology Department, Hospital Universitario de Jaén, Av. del Ejército Español, 10, 23007, Jaén, Spain
| | - Angelo Gámez-Pozo
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
- Biomedica Molecular Medicine SL, C/Faraday 7, 28049, Madrid, Spain
| | - Lucía Trilla-Fuertes
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - María Isabel Lumbreras-Herrera
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | | | - Carmen González-Olmedo
- Medical Oncology Department, Hospital Universitario de Jaén, Av. del Ejército Español, 10, 23007, Jaén, Spain
| | - Enrique Espinosa
- Medical Oncology Service, La Paz University Hospital-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
- Biomedical Research Networking Center On Oncology-CIBERONC, ISCIII, Av. Monforte de Lemos 5, 28029, Madrid, Spain
| | - Pilar Zamora
- Medical Oncology Service, La Paz University Hospital-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
- Biomedical Research Networking Center On Oncology-CIBERONC, ISCIII, Av. Monforte de Lemos 5, 28029, Madrid, Spain
| | - Pedro Sánchez-Rovira
- Medical Oncology Department, Hospital Universitario de Jaén, Av. del Ejército Español, 10, 23007, Jaén, Spain
| | - Juan Ángel Fresno Vara
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain.
- Biomedica Molecular Medicine SL, C/Faraday 7, 28049, Madrid, Spain.
- Biomedical Research Networking Center On Oncology-CIBERONC, ISCIII, Av. Monforte de Lemos 5, 28029, Madrid, Spain.
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Trilla-Fuertes L, Gámez-Pozo A, Nogué M, Busquier I, Arias F, López-Campos F, Fernández-Montes A, Ruiz A, Velázquez C, Martín-Bravo C, Pérez-Ruiz E, Asensio E, Hernández-Yagüe X, Rodrigues A, Ghanem I, López-Vacas R, Hafez A, Arias P, Dapía I, Solís M, Dittmann A, Ramos R, Llorens C, Maurel J, Campos-Barros Á, Fresno Vara JÁ, Feliu J. Utility of CYP2D6 copy number variants as prognostic biomarker in localized anal squamous cell carcinoma. Cancer 2023. [PMID: 37096763 DOI: 10.1002/cncr.34797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 04/26/2023]
Abstract
BACKGROUND Anal squamous cell carcinoma (ASCC) is an infrequent tumor whose treatment has not changed since the 1970s. The aim of this study is the identification of biomarkers allowing personalized treatments and improvement of therapeutic outcomes. METHODS Forty-six paraffin tumor samples from ASCC patients were analyzed by whole-exome sequencing. Copy number variants (CNVs) were identified and their relation to disease-free survival (DFS) was studied and validated in an independent retrospective cohort of 101 ASCC patients from the Multidisciplinary Spanish Digestive Cancer Group (GEMCAD). GEMCAD cohort proteomics allowed assessing the biological features of these tumors. RESULTS On the discovery cohort, the median age was 61 years old, 50% were males, stages I/II/III: 3 (7%)/16 (35%)/27 (58%), respectively, median DFS was 33 months, and overall survival was 45 months. Twenty-nine genes whose duplication was related to DFS were identified. The most representative was duplications of the CYP2D locus, including CYP2D6, CYP2D7P, and CYP2D8P genes. Patients with CYP2D6 CNV had worse DFS at 5 years than those with two CYP2D6 copies (21% vs. 84%; p < .0002, hazard ratio [HR], 5.8; 95% confidence interval [CI], 2.7-24.9). In the GEMCAD validation cohort, patients with CYP2D6 CNV also had worse DFS at 5 years (56% vs. 87%; p = .02, HR = 3.6; 95% CI, 1.1-5.7). Mitochondria and mitochondrial cell-cycle proteins were overexpressed in patients with CYP2D6 CNV. CONCLUSIONS Tumor CYP2D6 CNV identified patients with a significantly worse DFS at 5 years among localized ASCC patients treated with 5-fluorouracil, mitomycin C, and radiotherapy. Proteomics pointed out mitochondria and mitochondrial cell-cycle genes as possible therapeutic targets for these high-risk patients. PLAIN LANGUAGE SUMMARY Anal squamous cell carcinoma is an infrequent tumor whose treatment has not been changed since the 1970s. However, disease-free survival in late staged tumors is between 40% and 70%. The presence of an alteration in the number of copies of CYP2D6 gene is a biomarker of worse disease-free survival. The analysis of the proteins in these high-risk patients pointed out mitochondria and mitochondrial cell-cycle genes as possible therapeutic targets. Therefore, the determination of the number of copies of CYP2D6 allows the identification of anal squamous carcinoma patients with a high-risk of relapse that could be redirected to a clinical trial. Additionally, this study may be useful to suggest new treatment strategies to increase current therapy efficacy.
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Affiliation(s)
| | - Angelo Gámez-Pozo
- Molecular Oncology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
- Biomedica Molecular Medicine SL, Madrid, Spain
| | - Miguel Nogué
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital de Granollers, Barcelona, Spain
| | - Isabel Busquier
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Provincial de Castellón, Castellón, Spain
| | - Fernando Arias
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Radiotherapy Oncology Service, Complejo Hospitalario de Navarra, Navarra, Spain
| | - Fernando López-Campos
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Radiotherapy Oncology Service, Hospital Ramón y Cajal, Madrid, Spain
| | - Ana Fernández-Montes
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Complejo Hospitalario Universitario de Ourense, Ourense, Spain
| | - Ana Ruiz
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Universitario Puerta de Hierro Majadahonda, IDIPHISA, Madrid, Spain
| | - Concepción Velázquez
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Miguel Servet, Zaragoza, Spain
| | | | - Elisabeth Pérez-Ruiz
- Unidad de Gestión Clínica Intercentros de Oncología Médica, Hospitales Universitarios Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga, Hospitales Universitarios Regional y Virgen de la Victoria, Málaga, Spain
| | - Elena Asensio
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital General Universitario de Elche, Elche, Spain
| | - Xavier Hernández-Yagüe
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Instituto Catalán de Oncología-Girona, Girona, Spain
| | - Aline Rodrigues
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Ismael Ghanem
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Universitario La Paz, Madrid, Spain
| | - Rocío López-Vacas
- Molecular Oncology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Ahmed Hafez
- Biotechvana SL, Parque Científico de Madrid, Madrid, Spain
| | - Pedro Arias
- Pharmacogenetics Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Autonomous University of Madrid, Madrid, Spain
| | - Irene Dapía
- Pharmacogenetics Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Autonomous University of Madrid, Madrid, Spain
| | - Mario Solís
- Bioinformatics Unit, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Antje Dittmann
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Ricardo Ramos
- Genomics Unit, Parque Científico de Madrid, Madrid, Spain
| | - Carlos Llorens
- Biotechvana SL, Parque Científico de Madrid, Madrid, Spain
| | - Joan Maurel
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Department, Hospital Clínic of Barcelona, Translational Genomics and Targeted Therapeutics in Solid Tumors Group, IDIBAPS, University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
| | - Ángel Campos-Barros
- Institute of Medical and Molecular Genetics, IdiPAZ, Hospital Universitario La Paz/CIBERER Unit 753, ISCIII, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Molecular Oncology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
- Biomedica Molecular Medicine SL, Madrid, Spain
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
| | - Jaime Feliu
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Universitario La Paz, Madrid, Spain
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
- Cátedra UAM-Amgen, Universidad Autónoma de Madrid, Madrid, Spain
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5
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Miranda-Poma J, Trilla-Fuertes L, López-Vacas R, López-Camacho E, García-Fernández E, Pertejo A, Lumbreras-Herrera MI, Zapater-Moros A, Díaz-Almirón M, Dittmann A, Fresno Vara JÁ, Espinosa E, González-Peramato P, Pinto-Marín Á, Gámez-Pozo A. Proteomics Characterization of Clear Cell Renal Cell Carcinoma. J Clin Med 2023; 12:jcm12010384. [PMID: 36615183 PMCID: PMC9821535 DOI: 10.3390/jcm12010384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023] Open
Abstract
PURPOSE To explore the tumor proteome of patients diagnosed with localized clear cell renal cancer (ccRCC) and treated with surgery. MATERIAL AND METHODS A total of 165 FFPE tumor samples from patients diagnosed with ccRCC were analyzed using DIA-proteomics. Proteomics ccRCC subtypes were defined using a consensus cluster algorithm (CCA) and characterized by a functional approach using probabilistic graphical models and survival analyses. RESULTS We identified and quantified 3091 proteins, including 2026 high-confidence proteins. Two proteomics subtypes of ccRCC (CC1 and CC2) were identified by CC using the high-confidence proteins only. Characterization of molecular differences between CC1 and CC2 was performed in two steps. First, we defined 514 proteins showing differential expression between the two subtypes using a significance analysis of microarrays analysis. Proteins overexpressed in CC1 were mainly related to translation and ribosome, while proteins overexpressed in CC2 were mainly related to focal adhesion and membrane. Second, a functional analysis using probabilistic graphical models was performed. CC1 subtype is characterized by an increased expression of proteins related to glycolysis, mitochondria, translation, adhesion proteins related to cytoskeleton and actin, nucleosome, and spliceosome, while CC2 subtype showed higher expression of proteins involved in focal adhesion, extracellular matrix, and collagen organization. CONCLUSIONS ccRCC tumors can be classified in two different proteomics subtypes. CC1 and CC2 present specific proteomics profiles, reflecting alterations of different molecular pathways in each subtype. The knowledge generated in this type of studies could help in the development of new drugs targeting subtype-specific deregulated pathways.
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Affiliation(s)
- Jesús Miranda-Poma
- Medical Oncology Service, Hospital Universitario Quironsalud Madrid, 28223 Madrid, Spain
- Correspondence: (J.M.-P.); (A.G.-P.)
| | - Lucía Trilla-Fuertes
- Molecular Oncology Laboratory, Hospital Universitario La Paz—IdiPAZ, 28046 Madrid, Spain
| | - Rocío López-Vacas
- Molecular Oncology Laboratory, Hospital Universitario La Paz—IdiPAZ, 28046 Madrid, Spain
| | | | | | - Ana Pertejo
- Medical Oncology Service, Hospital Universitario La Paz, 28046 Madrid, Spain
| | | | | | | | - Antje Dittmann
- Functional Genomics Center Zurich, 8057 Zurich, Switzerland
| | - Juan Ángel Fresno Vara
- Molecular Oncology Laboratory, Hospital Universitario La Paz—IdiPAZ, 28046 Madrid, Spain
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, 28029 Madrid, Spain
| | - Enrique Espinosa
- Medical Oncology Service, Hospital Universitario La Paz, 28046 Madrid, Spain
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, 28029 Madrid, Spain
- Cátedra UAM-Amgen, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | | | - Álvaro Pinto-Marín
- Medical Oncology Service, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Angelo Gámez-Pozo
- Molecular Oncology Laboratory, Hospital Universitario La Paz—IdiPAZ, 28046 Madrid, Spain
- Biomedica Molecular Medicine SL, 28049 Madrid, Spain
- Correspondence: (J.M.-P.); (A.G.-P.)
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6
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Trilla-Fuertes L, Gámez-Pozo A, Lumbreras-Herrera MI, López-Vacas R, Heredia-Soto V, Ghanem I, López-Camacho E, Zapater-Moros A, Miguel M, Peña-Burgos EM, Palacios E, de Uribe M, Guerra L, Dittmann A, Mendiola M, Fresno Vara JÁ, Feliu J. Identification of Carcinogenesis and Tumor Progression Processes in Pancreatic Ductal Adenocarcinoma Using High-Throughput Proteomics. Cancers (Basel) 2022; 14:cancers14102414. [PMID: 35626021 PMCID: PMC9139847 DOI: 10.3390/cancers14102414] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 04/20/2022] [Revised: 05/05/2022] [Accepted: 05/11/2022] [Indexed: 11/16/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease with an overall 5-year survival rate of just 5%. A better understanding of the carcinogenesis processes and the mechanisms of the progression of PDAC is mandatory. Fifty-two PDAC patients treated with surgery and adjuvant therapy, with available primary tumors, normal tissue, preneoplastic lesions (PanIN), and/or lymph node metastases, were selected for the study. Proteins were extracted from small punches and analyzed by LC-MS/MS using data-independent acquisition. Proteomics data were analyzed using probabilistic graphical models, allowing functional characterization. Comparisons between groups were made using linear mixed models. Three proteomic tumor subtypes were defined. T1 (32% of patients) was related to adhesion, T2 (34%) had metabolic features, and T3 (34%) presented high splicing and nucleoplasm activity. These proteomics subtypes were validated in the PDAC TCGA cohort. Relevant biological processes related to carcinogenesis and tumor progression were studied in each subtype. Carcinogenesis in the T1 subtype seems to be related to an increase of adhesion and complement activation node activity, whereas tumor progression seems to be related to nucleoplasm and translation nodes. Regarding the T2 subtype, it seems that metabolism and, especially, mitochondria act as the motor of cancer development. T3 analyses point out that nucleoplasm, mitochondria and metabolism, and extracellular matrix nodes could be involved in T3 tumor carcinogenesis. The identified processes were different among proteomics subtypes, suggesting that the molecular motor of the disease is different in each subtype. These differences can have implications for the development of future tailored therapeutic approaches for each PDAC proteomics subtype.
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Affiliation(s)
- Lucía Trilla-Fuertes
- Molecular Oncology & Pathology Laboratory, Instituto de Genética Médica y Molecular-INGEMM, Hospital Universitario La Paz-IdiPAZ, 28046 Madrid, Spain; (L.T.-F.); (A.G.-P.); (M.I.L.-H.); (R.L.-V.); (J.Á.F.V.)
| | - Angelo Gámez-Pozo
- Molecular Oncology & Pathology Laboratory, Instituto de Genética Médica y Molecular-INGEMM, Hospital Universitario La Paz-IdiPAZ, 28046 Madrid, Spain; (L.T.-F.); (A.G.-P.); (M.I.L.-H.); (R.L.-V.); (J.Á.F.V.)
| | - María Isabel Lumbreras-Herrera
- Molecular Oncology & Pathology Laboratory, Instituto de Genética Médica y Molecular-INGEMM, Hospital Universitario La Paz-IdiPAZ, 28046 Madrid, Spain; (L.T.-F.); (A.G.-P.); (M.I.L.-H.); (R.L.-V.); (J.Á.F.V.)
| | - Rocío López-Vacas
- Molecular Oncology & Pathology Laboratory, Instituto de Genética Médica y Molecular-INGEMM, Hospital Universitario La Paz-IdiPAZ, 28046 Madrid, Spain; (L.T.-F.); (A.G.-P.); (M.I.L.-H.); (R.L.-V.); (J.Á.F.V.)
| | - Victoria Heredia-Soto
- Molecular Pathology and Therapeutic Targets Group, Hospital Universitario La Paz-IdiPAZ, 28046 Madrid, Spain; (V.H.-S.); (M.M.); (M.M.)
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, 28029 Madrid, Spain
| | - Ismael Ghanem
- Medical Oncology Service, Hospital Universitario La Paz, 28046 Madrid, Spain;
| | | | | | - María Miguel
- Molecular Pathology and Therapeutic Targets Group, Hospital Universitario La Paz-IdiPAZ, 28046 Madrid, Spain; (V.H.-S.); (M.M.); (M.M.)
| | - Eva M. Peña-Burgos
- Pathology Department, Hospital Universitario La Paz, 28046 Madrid, Spain; (E.M.P.-B.); (E.P.); (M.d.U.); (L.G.)
| | - Elena Palacios
- Pathology Department, Hospital Universitario La Paz, 28046 Madrid, Spain; (E.M.P.-B.); (E.P.); (M.d.U.); (L.G.)
| | - Marta de Uribe
- Pathology Department, Hospital Universitario La Paz, 28046 Madrid, Spain; (E.M.P.-B.); (E.P.); (M.d.U.); (L.G.)
| | - Laura Guerra
- Pathology Department, Hospital Universitario La Paz, 28046 Madrid, Spain; (E.M.P.-B.); (E.P.); (M.d.U.); (L.G.)
| | - Antje Dittmann
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, 8057 Zurich, Switzerland;
| | - Marta Mendiola
- Molecular Pathology and Therapeutic Targets Group, Hospital Universitario La Paz-IdiPAZ, 28046 Madrid, Spain; (V.H.-S.); (M.M.); (M.M.)
| | - Juan Ángel Fresno Vara
- Molecular Oncology & Pathology Laboratory, Instituto de Genética Médica y Molecular-INGEMM, Hospital Universitario La Paz-IdiPAZ, 28046 Madrid, Spain; (L.T.-F.); (A.G.-P.); (M.I.L.-H.); (R.L.-V.); (J.Á.F.V.)
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, 28029 Madrid, Spain
| | - Jaime Feliu
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, 28029 Madrid, Spain
- Medical Oncology Service, Hospital Universitario La Paz, 28046 Madrid, Spain;
- Cátedra UAM-ANGEM, Faculty of Medicine, Universidad Autónoma de Madrid, 28046 Madrid, Spain
- Correspondence:
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7
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López-Camacho E, Trilla-Fuertes L, Gámez-Pozo A, Dapía I, López-Vacas R, Zapater-Moros A, Lumbreras-Herrera MI, Arias P, Zamora P, Vara JÁF, Espinosa E. Synergistic effect of antimetabolic and chemotherapy drugs in triple-negative breast cancer. Biomed Pharmacother 2022; 149:112844. [PMID: 35339109 DOI: 10.1016/j.biopha.2022.112844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 11/02/2022] Open
Abstract
The triple-negative breast cancer (TNBC) subtype comprises approximately 15% of all breast cancers and is associated with poor long-term outcomes. Classical chemotherapy remains the standard of treatment, with toxicity and resistance being major limitations. TNBC is a high metabolic group, and antimetabolic drugs are effective in inhibiting TNBC cell growth. We analyzed the combined effect of chemotherapy and antimetabolic drug combinations in MDA-MB-231, MDA-MB-468 and HCC1143 human TNBC cell lines. Cells were treated with each drug or with drug combinations at a range of concentrations to establish the half-maximal inhibitory concentrations (IC50). The dose-effects of each drug or drug combination were calculated, and the synergistic or antagonistic effects of drug combinations were defined. Chemotherapy and antimetabolic drugs exhibited growth inhibitory effects on TNBC cell lines. Antimetabolic drugs targeting the glycolysis pathway had a synergistic effect with chemotherapy drugs, and antiglycolysis drug combinations also had a synergistic effect. The use of these drug combinations could lead to new therapeutic strategies that reduce chemotherapy drug doses, decreasing their toxic effect, or that maintain the doses but enhance their efficacy by their synergistic effect with other drugs.
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Affiliation(s)
- Elena López-Camacho
- Molecular Oncology Lab, La Paz University Hospital-IdiPAZ, Madrid, Spain; Biomedica Molecular Medicine SL, Madrid, Spain
| | | | - Angelo Gámez-Pozo
- Molecular Oncology Lab, La Paz University Hospital-IdiPAZ, Madrid, Spain; Biomedica Molecular Medicine SL, Madrid, Spain
| | - Irene Dapía
- Pharmacogenetics Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Autonomous University of Madrid, Madrid, Spain; Biomedical Research Networking Center on Rare Diseases-CIBERER, ISCIII, Madrid, Spain
| | - Rocío López-Vacas
- Molecular Oncology Lab, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Andrea Zapater-Moros
- Biomedica Molecular Medicine SL, Madrid, Spain; Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
| | | | - Pedro Arias
- Pharmacogenetics Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Autonomous University of Madrid, Madrid, Spain; Biomedical Research Networking Center on Rare Diseases-CIBERER, ISCIII, Madrid, Spain
| | - Pilar Zamora
- Medical Oncology Service, La Paz University Hospital, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Molecular Oncology Lab, La Paz University Hospital-IdiPAZ, Madrid, Spain; Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
| | - Enrique Espinosa
- Medical Oncology Service, La Paz University Hospital, Madrid, Spain; Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain.
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8
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García-Adrián S, Trilla-Fuertes L, Gámez-Pozo A, Chiva C, López-Vacas R, López-Camacho E, Zapater-Moros A, Lumbreras-Herrera MI, Hardisson D, Yébenes L, Zamora P, Sabidó E, Fresno Vara JÁ, Espinosa E. Molecular characterization of triple negative breast cancer formaldehyde-fixed paraffin-embedded samples by data-independent acquisition proteomics. Proteomics 2021; 22:e2100110. [PMID: 34624180 DOI: 10.1002/pmic.202100110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 09/14/2021] [Accepted: 09/29/2021] [Indexed: 11/05/2022]
Abstract
Triple negative breast cancer accounts for 15%-20% of all breast carcinomas and is clinically characterized by an aggressive phenotype and poor prognosis. Triple negative tumors do not benefit from targeted therapies, so further characterization is needed to define subgroups with potential therapeutic value. In this work, the proteomes of 125 formalin-fixed paraffin-embedded samples from patients diagnosed with non-metastatic triple negative breast cancer were analyzed using data-independent acquisition + in a LTQ-Orbitrap Fusion Lumos mass spectrometer coupled to an EASY-nLC 1000. 1206 proteins were identified in at least 66% of the samples. Hierarchical clustering, probabilistic graphical models and Significance Analysis of Microarrays were combined to characterize proteomics-based molecular groups. Two molecular groups were defined with differences in biological processes such as glycolysis, translation and immune response. These two molecular groups showed also several differentially expressed proteins. This clinically homogenous dataset may serve to design new therapeutic strategies in the future.
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Affiliation(s)
| | | | - Angelo Gámez-Pozo
- Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Cristina Chiva
- Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Rocío López-Vacas
- Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | | | | | - María I Lumbreras-Herrera
- Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - David Hardisson
- Molecular Pathology and Therapeutic Targets Group, La Paz University Hospital (IdiPAZ), Madrid, Spain.,Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain.,Faculty of Medicine, Universidad Autónoma de Madrid, Madrid, Spain.,Department of Pathology, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Laura Yébenes
- Molecular Pathology and Therapeutic Targets Group, La Paz University Hospital (IdiPAZ), Madrid, Spain
| | - Pilar Zamora
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain.,Medical Oncology Service, La Paz University Hospital-IdiPAZ, Madrid, Spain.,Cátedra UAM-Amgen, Universidad Autónoma de Madrid, Madrid, Spain
| | - Eduard Sabidó
- Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Juan Ángel Fresno Vara
- Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain.,Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
| | - Enrique Espinosa
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain.,Medical Oncology Service, La Paz University Hospital-IdiPAZ, Madrid, Spain.,Cátedra UAM-Amgen, Universidad Autónoma de Madrid, Madrid, Spain
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9
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Trilla-Fuertes L, Gámez-Pozo A, Maurel J, Garcia-Carbonero R, Capdevila J, G-Pastrián L, Mendiola M, Peña C, López-Vacas R, Cuatrecasas M, García-Alfonso P, Ramos-Ruiz R, Llorens C, Ghanem I, Conill C, Heredia-Soto V, Campos-Barros Á, Fresno Vara JÁ, Feliu J. Description of the genetic variants identified in a cohort of patients diagnosed with localized anal squamous cell carcinoma and treated with panitumumab. Sci Rep 2021; 11:7402. [PMID: 33795829 PMCID: PMC8016846 DOI: 10.1038/s41598-021-86966-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 03/11/2021] [Indexed: 11/09/2022] Open
Abstract
Squamous cell carcinoma is the most frequent histologic type of anal carcinoma. The standard of care since the 1970s has been a combination of 5-fluorouracil, mitomycin C, and radiotherapy. This treatment is very effective in T1/T2 tumors (achieving complete regression in 80–90% of tumors). However, in T3/T4 tumors, the 3-year relapse free survival rate is only 50%. The VITAL trial aimed to assess the efficacy and safety of panitumumab in combination with this standard treatment. In this study, 27 paraffin-embedded samples from the VITAL trial and 18 samples from patients from daily clinical practice were analyzed by whole-exome sequencing and the influence of the presence of genetic variants in the response to panitumumab was studied. Having a moderate- or high-impact genetic variant in PIK3CA seemed to be related to the response to panitumumab. Furthermore, copy number variants in FGFR3, GRB2 and JAK1 were also related to the response to panitumumab. These genetic alterations have also been studied in the cohort of patients from daily clinical practice (not treated with panitumumab) and they did not have a predictive value. Therefore, in this study, a collection of genetic alterations related to the response with panitumumab was described. These results could be useful for patient stratification in new anti-EGFR clinical trials.
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Affiliation(s)
| | - Angelo Gámez-Pozo
- Biomedica Molecular Medicine SL, Madrid, Spain.,Molecular Oncology and Pathology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Joan Maurel
- Medical Oncology Department, Hospital Clinic of Barcelona, Translational Genomics and Targeted Therapeutics in Solid Tumors Group, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Rocio Garcia-Carbonero
- Medical Oncology Department, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), UCM, CNIO, CIBERONC, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Jaume Capdevila
- Medical Oncology Service, Vall Hebron Institute of Oncology (VHIO), Vall Hebron University Hospital, Barcelona, Spain
| | - Laura G-Pastrián
- Pathology Department, Hospital Universitario La Paz, Madrid, Spain.,Molecular Pathology and Therapeutic Targets Group, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Marta Mendiola
- Molecular Pathology and Therapeutic Targets Group, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain.,Biomedical Research Networking Center On Oncology-CIBERONC, ISCIII, Madrid, Spain
| | - Cristina Peña
- Pathology Department, Hospital Universitario La Paz, Madrid, Spain
| | - Rocío López-Vacas
- Molecular Oncology and Pathology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Miriam Cuatrecasas
- Pathology Department, Hospital Clínic Universitat de Barcelona, Villarroel 170, 08036, Barcelona, Spain
| | - Pilar García-Alfonso
- Medical Oncology Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Ricardo Ramos-Ruiz
- Genomics Unit Cantoblanco, Parque Científico de Madrid, C/ Faraday 7, 28049, Madrid, Spain
| | - Carlos Llorens
- Biotechvana SL, Parque Científico de Madrid, C/ Faraday 7, 28049, Madrid, Spain
| | - Ismael Ghanem
- Medical Oncology Department, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Carles Conill
- Radiotherapy Oncology Department, Hospital Clinic of Barcelona, Carrer de Villarroel 170, 08036, Barcelona, Spain
| | - Victoria Heredia-Soto
- Biomedical Research Networking Center On Oncology-CIBERONC, ISCIII, Madrid, Spain.,Translational Oncology Group, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Ángel Campos-Barros
- Institute of Medical and Molecular Genetics, IdiPAZ, Unit 753, ISCIII, Hospital Universitario La Paz /& CIBERER, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Molecular Oncology and Pathology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain.,Biomedical Research Networking Center On Oncology-CIBERONC, ISCIII, Madrid, Spain
| | - Jaime Feliu
- Biomedical Research Networking Center On Oncology-CIBERONC, ISCIII, Madrid, Spain. .,Medical Oncology Department, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain. .,Cátedra UAM-Amgen, Universidad Autónoma de Madrid, Madrid, Spain.
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10
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Trilla-Fuertes L, Gámez-Pozo A, Arevalillo JM, López-Vacas R, López-Camacho E, Prado-Vázquez G, Zapater-Moros A, Díaz-Almirón M, Ferrer-Gómez M, Navarro H, Nanni P, Zamora P, Espinosa E, Maín P, Fresno Vara JÁ. Bayesian networks established functional differences between breast cancer subtypes. PLoS One 2020; 15:e0234752. [PMID: 32525929 PMCID: PMC7289386 DOI: 10.1371/journal.pone.0234752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 06/01/2020] [Indexed: 12/15/2022] Open
Abstract
Breast cancer is a heterogeneous disease. In clinical practice, tumors are classified as hormonal receptor positive, Her2 positive and triple negative tumors. In previous works, our group defined a new hormonal receptor positive subgroup, the TN-like subtype, which had a prognosis and a molecular profile more similar to triple negative tumors. In this study, proteomics and Bayesian networks were used to characterize protein relationships in 96 breast tumor samples. Components obtained by these methods had a clear functional structure. The analysis of these components suggested differences in processes such as mitochondrial function or extracellular matrix between breast cancer subtypes, including our new defined subtype TN-like. In addition, one of the components, mainly related with extracellular matrix processes, had prognostic value in this cohort. Functional approaches allow to build hypotheses about regulatory mechanisms and to establish new relationships among proteins in the breast cancer context.
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Affiliation(s)
| | - Angelo Gámez-Pozo
- Biomedica Molecular Medicine SL, Madrid, Spain
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Jorge M. Arevalillo
- Operational Research and Numerical Analysis, National Distance Education University (UNED), Madrid, Spain
| | - Rocío López-Vacas
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | | | - Guillermo Prado-Vázquez
- Biomedica Molecular Medicine SL, Madrid, Spain
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Andrea Zapater-Moros
- Biomedica Molecular Medicine SL, Madrid, Spain
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | | | - María Ferrer-Gómez
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Hilario Navarro
- Operational Research and Numerical Analysis, National Distance Education University (UNED), Madrid, Spain
| | - Paolo Nanni
- Functional Genomics Centre Zurich, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Pilar Zamora
- Medical Oncology Service, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Enrique Espinosa
- Medical Oncology Service, La Paz University Hospital-IdiPAZ, Madrid, Spain
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
| | - Paloma Maín
- Department of Statistics and Operations Research, Faculty of Mathematics, Complutense University of Madrid, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Biomedica Molecular Medicine SL, Madrid, Spain
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
- * E-mail:
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11
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Trilla-Fuertes L, Ghanem I, Maurel J, G-Pastrián L, Mendiola M, Peña C, López-Vacas R, Prado-Vázquez G, López-Camacho E, Zapater-Moros A, Heredia V, Cuatrecasas M, García-Alfonso P, Capdevila J, Conill C, García-Carbonero R, Heath KE, Ramos-Ruiz R, Llorens C, Campos-Barros Á, Gámez-Pozo A, Feliu J, Vara JÁF. Comprehensive Characterization of the Mutational Landscape in Localized Anal Squamous Cell Carcinoma. Transl Oncol 2020; 13:100778. [PMID: 32422573 PMCID: PMC7229291 DOI: 10.1016/j.tranon.2020.100778] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/02/2020] [Indexed: 12/21/2022] Open
Abstract
Anal squamous cell carcinoma (ASCC) is a rare neoplasm. Chemoradiotherapy is the standard of care, with no therapeutic advances achieved over the past three decades. Thus, a deeper molecular characterization of this disease is still necessary. We analyzed 46 paraffin-embedded tumor samples from patients diagnosed with primary ASCC by exome sequencing. A bioinformatics approach focused in the identification of high-impact genetic variants, which may act as drivers of oncogenesis, was performed. The relation between genetics variants and prognosis was also studied. The list of high-impact genetic variants was unique for each patient. However, the pathways in which these genes are involved are well-known hallmarks of cancer, such as angiogenesis or immune pathways. Additionally, we determined that genetic variants in BRCA2, ZNF750, FAM208B, ZNF599, and ZC3H13 genes are related with poor disease-free survival in ASCC. This may help to stratify the patient's prognosis and open new avenues for potential therapeutic intervention. In conclusion, sequencing of ASCC clinical samples appears an encouraging tool for the molecular portrait of this disease.
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Affiliation(s)
| | - Ismael Ghanem
- Medical Oncology Department, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Joan Maurel
- Medical Oncology Department, Hospital Clinic of Barcelona, Translational Genomics and Targeted Therapeutics in Solid Tumors Group, IDIBAPS, University of Barcelona, Carrer de Villarroel 170, 08036, Barcelona, Spain
| | - Laura G-Pastrián
- Pathology Department, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain; Molecular Pathology and Therapeutic Targets Group, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Marta Mendiola
- Molecular Pathology and Therapeutic Targets Group, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain; Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Av. Monforte de Lemos 5, 28029, Madrid, Spain
| | - Cristina Peña
- Pathology Department, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Rocío López-Vacas
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | | | - Elena López-Camacho
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Andrea Zapater-Moros
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Victoria Heredia
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Av. Monforte de Lemos 5, 28029, Madrid, Spain; Translational Oncology Lab, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Miriam Cuatrecasas
- Pathology Department, Hospital Clínic Universitari de Barcelona, Carrer de Villarroel 170, 08036, Barcelona, Spain
| | - Pilar García-Alfonso
- Medical Oncology Department, Hospital General Universitario Gregorio Marañón, C/ Dr Esquerdo 46, 28007, Madrid, Spain
| | - Jaume Capdevila
- Medical Oncology Service, Vall Hebron University Hospital. Vall Hebron Institute of Oncology (VHIO), Passeig de la Vall d'Hebron, 119-129, 08035, Barcelona, Spain
| | - Carles Conill
- Radiotherapy Oncology Department, Hospital Clínic Universitari de Barcelona, Carrer de Villarroel 170, 08036, Barcelona, Spain
| | - Rocío García-Carbonero
- Medical Oncology Department, Hospital Universitario 12 de Ocubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), UCM, CNIO, CIBERONC, Av. Córdoba s/n, 28041, Madrid, Spain
| | - Karen E Heath
- Institute of Medical and Molecular Genetics, IdiPAZ, Hospital Universitario La Paz /& CIBERER, Unit 753, ISCIII, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Ricardo Ramos-Ruiz
- Genomics Unit Cantoblanco, Parque Científico de Madrid, C/ Faraday 7, 28049, Madrid, Spain
| | - Carlos Llorens
- Biotechvana SL, Parque Científico de Madrid, C/ Faraday 7, 28049, Madrid, Spain
| | - Ángel Campos-Barros
- Institute of Medical and Molecular Genetics, IdiPAZ, Hospital Universitario La Paz /& CIBERER, Unit 753, ISCIII, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Angelo Gámez-Pozo
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Jaime Feliu
- Medical Oncology Department, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain; Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Av. Monforte de Lemos 5, 28029, Madrid, Spain; Cátedra UAM-Amgen, Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain.
| | - Juan Ángel Fresno Vara
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Av. Monforte de Lemos 5, 28029, Madrid, Spain; Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain.
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12
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Trilla-Fuertes L, Gámez-Pozo A, López-Camacho E, Prado-Vázquez G, Zapater-Moros A, López-Vacas R, Arevalillo JM, Díaz-Almirón M, Navarro H, Maín P, Espinosa E, Zamora P, Fresno Vara JÁ. Computational models applied to metabolomics data hints at the relevance of glutamine metabolism in breast cancer. BMC Cancer 2020; 20:307. [PMID: 32293335 PMCID: PMC7265650 DOI: 10.1186/s12885-020-06764-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 03/19/2020] [Indexed: 01/25/2023] Open
Abstract
Background Metabolomics has a great potential in the development of new biomarkers in cancer and it has experiment recent technical advances. Methods In this study, metabolomics and gene expression data from 67 localized (stage I to IIIB) breast cancer tumor samples were analyzed, using (1) probabilistic graphical models to define associations using quantitative data without other a priori information; and (2) Flux Balance Analysis and flux activities to characterize differences in metabolic pathways. Results On the one hand, both analyses highlighted the importance of glutamine in breast cancer. Moreover, cell experiments showed that treating breast cancer cells with drugs targeting glutamine metabolism significantly affects cell viability. On the other hand, these computational methods suggested some hypotheses and have demonstrated their utility in the analysis of metabolomics data and in associating metabolomics with patient’s clinical outcome. Conclusions Computational analyses applied to metabolomics data suggested that glutamine metabolism is a relevant process in breast cancer. Cell experiments confirmed this hypothesis. In addition, these computational analyses allow associating metabolomics data with patient prognosis.
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Affiliation(s)
| | - Angelo Gámez-Pozo
- Biomedica Molecular Medicine SL, C/ Faraday, 7, 28049, Madrid, Spain.,Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain
| | - Elena López-Camacho
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain
| | | | - Andrea Zapater-Moros
- Biomedica Molecular Medicine SL, C/ Faraday, 7, 28049, Madrid, Spain.,Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain
| | - Rocío López-Vacas
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain
| | - Jorge M Arevalillo
- Department of Statistics, Operational Research and Numerical Analysis, National University of Distance Education (UNED), Paseo Senda del Rey, 9, 28040, Madrid, Spain
| | - Mariana Díaz-Almirón
- Biostatistics Unit, La Paz University Hospital-IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain
| | - Hilario Navarro
- Department of Statistics, Operational Research and Numerical Analysis, National University of Distance Education (UNED), Paseo Senda del Rey, 9, 28040, Madrid, Spain
| | - Paloma Maín
- Department of Statistics and Operations Research, Faculty of Mathematics, Complutense University of Madrid, Plaza de las Ciencias, 3, 28040, Madrid, Spain
| | - Enrique Espinosa
- Medical Oncology Service, La Paz University Hospital-IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain.,Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, C/Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Pilar Zamora
- Medical Oncology Service, La Paz University Hospital-IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain.,Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, C/Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain. .,Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, C/Melchor Fernández Almagro, 3, 28029, Madrid, Spain.
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13
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Trilla-Fuertes L, Ghanem I, Gámez-Pozo A, Maurel J, G-Pastrián L, Mendiola M, Peña C, López-Vacas R, Prado-Vázquez G, López-Camacho E, Zapater-Moros A, Heredia V, Cuatrecasas M, García-Alfonso P, Capdevila J, Conill C, García-Carbonero R, Ramos-Ruiz R, Fortes C, Llorens C, Nanni P, Fresno Vara JÁ, Feliu J. Genetic Profile and Functional Proteomics of Anal Squamous Cell Carcinoma: Proposal for a Molecular Classification. Mol Cell Proteomics 2020; 19:690-700. [PMID: 32107283 PMCID: PMC7124473 DOI: 10.1074/mcp.ra120.001954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Indexed: 12/21/2022] Open
Abstract
Anal squamous cell carcinoma is a rare tumor. Chemo-radiotherapy yields a 50% 3-year relapse-free survival rate in advanced anal cancer, so improved predictive markers and therapeutic options are needed. High-throughput proteomics and whole-exome sequencing were performed in 46 paraffin samples from anal squamous cell carcinoma patients. Hierarchical clustering was used to establish groups de novo Then, probabilistic graphical models were used to study the differences between groups of patients at the biological process level. A molecular classification into two groups of patients was established, one group with increased expression of proteins related to adhesion, T lymphocytes and glycolysis; and the other group with increased expression of proteins related to translation and ribosomes. The functional analysis by the probabilistic graphical model showed that these two groups presented differences in metabolism, mitochondria, translation, splicing and adhesion processes. Additionally, these groups showed different frequencies of genetic variants in some genes, such as ATM, SLFN11 and DST Finally, genetic and proteomic characteristics of these groups suggested the use of some possible targeted therapies, such as PARP inhibitors or immunotherapy.
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Affiliation(s)
| | - Ismael Ghanem
- Medical Oncology Department, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Angelo Gámez-Pozo
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz -IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Joan Maurel
- Medical Oncology Department, Hospital Clinic of Barcelona, Translational Genomics and Targeted Therapeutics in Solid Tumors Group, IDIBAPS, University of Barcelona, Carrer de Villarroel 170, 08036, Barcelona, Spain
| | - Laura G-Pastrián
- Pathology Department, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain; Molecular Pathology and Therapeutic Targets Group, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Marta Mendiola
- Molecular Pathology and Therapeutic Targets Group, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain; Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Av. Monforte de Lemos 5, 28029, Madrid, Spain
| | - Cristina Peña
- Pathology Department, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Rocío López-Vacas
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz -IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | | | - Elena López-Camacho
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz -IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Andrea Zapater-Moros
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz -IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Victoria Heredia
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Av. Monforte de Lemos 5, 28029, Madrid, Spain; Translational Oncology Lab, Hospital Universitario La Paz -IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Miriam Cuatrecasas
- Pathology Department, Hospital Clínic Universitari de Barcelona, Carrer de Villarroel 170, 08036, Barcelona, Spain
| | - Pilar García-Alfonso
- Medical Oncology Department, Hospital General Universitario Gregorio Marañón, /Dr. Esquerdo 46, 28007, Madrid, Spain
| | - Jaume Capdevila
- Medical Oncology Service, Vall Hebron University Hospital. Vall Hebron Institute of Oncology (VHIO), Paseigg de la Vall d'Hebron 119, 08035, Barcelona, Spain
| | - Carles Conill
- Radiotherapy Oncology Department, Hospital Clínic Universitari de Barcelona, Carrer de Villarroel 170, 08036, Barcelona, Spain
| | - Rocío García-Carbonero
- Medical Oncology Service, Hospital Universitario 12 de Ocubre, Av. de Córdoba s/n, 28041, Madrid, Spain
| | - Ricardo Ramos-Ruiz
- Genomics Unit Cantoblanco, Parque Científico de Madrid, C/ Faraday 7, 28049, Madrid, Spain
| | - Claudia Fortes
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Carlos Llorens
- Biotechvana SL, Parque Científico de Madrid, C/ Faraday 7, 28049, Madrid, Spain
| | - Paolo Nanni
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Juan Ángel Fresno Vara
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz -IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain; Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Av. Monforte de Lemos 5, 28029, Madrid, Spain
| | - Jaime Feliu
- Medical Oncology Department, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain; Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Av. Monforte de Lemos 5, 28029, Madrid, Spain; Cátedra UAM-Amgen, Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain.
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14
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Trilla-Fuertes L, Miranda N, Castellano D, López-Vacas R, Farfán Tello CA, de Velasco G, Villacampa F, López-Camacho E, Prado-Vázquez G, Zapater-Moros A, Espinosa E, Fresno Vara JÁ, Pinto Á, Gámez-Pozo A. miRNA profiling in renal carcinoma suggest the existence of a group of pro-angionenic tumors in localized clear cell renal carcinoma. PLoS One 2020; 15:e0229075. [PMID: 32109249 PMCID: PMC7048408 DOI: 10.1371/journal.pone.0229075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 12/05/2019] [Accepted: 01/28/2020] [Indexed: 11/18/2022] Open
Abstract
Renal cell carcinoma comprises a variety of entities, the most common being the clear-cell, papillary and chromophobe subtypes. These subtypes are related to different clinical evolution; however, most therapies have been developed for clear-cell carcinoma and there is not a specific treatment based on different subtypes. In this study, one hundred and sixty-four paraffin samples from primary nephrectomies for localized tumors were analyzed. MiRNAs were isolated and measured by microRNA arrays. Significance Analysis of Microarrays and Consensus Cluster algorithm were used to characterize different renal subtypes. The analyses showed that chromophobe renal tumors are a homogeneous group characterized by an overexpression of miR 1229, miR 10a, miR 182, miR 1208, miR 222, miR 221, miR 891b, miR 629-5p and miR 221-5p. On the other hand, clear cell renal carcinomas presented two different groups inside this histological subtype, with differences in miRNAs that regulate focal adhesion, transcription, apoptosis and angiogenesis processes. Specifically, one of the defined groups had an overexpression of proangiogenic microRNAs miR185, miR126 and miR130a. In conclusion, differences in miRNA expression profiles between histological renal subtypes were established. In addition, clear cell renal carcinomas had different expression of proangiogenic miRNAs. With the emergence of antiangiogenic drugs, these differences could be used as therapeutic targets in the future or as a selection method for tailoring personalized treatments.
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Affiliation(s)
| | - Natalia Miranda
- Urology Service, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Daniel Castellano
- Medical Oncology Service, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Rocío López-Vacas
- Molecular Oncology and Pathology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Carlos A Farfán Tello
- Medical Oncology Service, Hospital Universitario 12 de Octubre, Madrid, Spain.,Clínica Internacional S.A., Lima, Perú
| | | | | | | | - Guillermo Prado-Vázquez
- Biomedica Molecular Medicine SL, Madrid, Spain.,Molecular Oncology and Pathology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Andrea Zapater-Moros
- Biomedica Molecular Medicine SL, Madrid, Spain.,Molecular Oncology and Pathology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain.,Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
| | - Enrique Espinosa
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain.,Medical Oncology Service, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Biomedica Molecular Medicine SL, Madrid, Spain.,Molecular Oncology and Pathology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain.,Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
| | - Álvaro Pinto
- Medical Oncology Service, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Angelo Gámez-Pozo
- Biomedica Molecular Medicine SL, Madrid, Spain.,Molecular Oncology and Pathology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
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15
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Auñon PZ, Adrián SG, Trilla-Fuertes L, Gámez-Pozo A, Prado-Vázquez G, Zapater-Moros A, Almirón MD, Vacas RL, Chiva C, Chiva C, Sabidó E, Arranz EE, Vara JÁF. Abstract P3-08-42: Disease-free survival prognostic signature in triple-negative breast cancer based on high-throughput proteomics data. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p3-08-42] [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 Triple negative breast cancer (TNBC) accounts for 15-20% of the breast cancer and is characterized by an aggressive phenotype and worst prognosis. TNBC does not benefit from any targeted therapy, so further characterization would be needed to define subgroups with potential therapeutic value. Material and methods 125 TNBC paraffin samples were analyzed using high-throughput proteomics based on SWATH-MS. Survival analyses and a prognostic predictor were done using BRB Array Tools. Proteins related with disease-free survival were established and, then, a prognostic signature was built based on their p-values. Results and discussion Using SWATH-MS, 1,206 proteins were identified in a cohort of 125 TNBC tumors. Of these 1,206 proteins, 29 proteins were related with disease-free survival. In addition, a prognostic signature based on the expression of two proteins, RMB3 and NIPSNAP1, was defined. The predictor split our population into a low-risk and a high-risk group (p=0.0002, HR= 6.519). Multivariate analysis showed that the prognostic signature based on the expression of these two proteins supplied significant information to the clinical parameters. Conclusion SWATH-MS proteomics demonstrates its utility in the analysis of TNBC paraffin samples. Moreover, this proteomics data allows us to build a prognostic signature based on the expression of two proteins (RBM3 and NIPSNAP1). This prognostic signature could be used in the future to identify a population with a high-risk of relapse that may be directed to a clinical trial.
Citation Format: Pilar Zamora Auñon, Silvia García Adrián, Lucia Trilla-Fuertes, Angelo Gámez-Pozo, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Mariana Díaz- Almirón, Rocío López Vacas, Cristina Chiva, Cristina Chiva, Eduard Sabidó, Enrique Espinosa Arranz, Juan Ángel Fresno Vara. Disease-free survival prognostic signature in triple-negative breast cancer based on high-throughput proteomics data [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-08-42.
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Affiliation(s)
| | | | | | - Angelo Gámez-Pozo
- 4Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM. Hospital La Paz., Madrid, Spain
| | | | - Andrea Zapater-Moros
- 6Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Madrid, Spain
| | | | - Rocío López Vacas
- 8Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Cristina Chiva
- 9Proteomics Unit, Center for Genomics Regulation, Institute of Science and Technology (BIST)., Barcelona, Spain
| | - Cristina Chiva
- 9Proteomics Unit, Center for Genomics Regulation, Institute of Science and Technology (BIST)., Barcelona, Spain
| | - Eduard Sabidó
- 10Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology (BIST)., Barcelona, Spain
| | | | - Juan Ángel Fresno Vara
- 8Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
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Trilla-Fuertes L, Gámez-Pozo A, Díaz-Almirón M, Prado-Vázquez G, Zapater-Moros A, López-Vacas R, Nanni P, Zamora P, Espinosa E, Fresno Vara JÁ. Computational metabolism modeling predicts risk of distant relapse-free survival in breast cancer patients. Future Oncol 2019; 15:3483-3490. [PMID: 31580166 DOI: 10.2217/fon-2018-0698] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Aim: Differences in metabolism among breast cancer subtypes suggest that metabolism plays an important role in this disease. Flux balance analysis is used to explore these differences as well as drug response. Materials & methods: Proteomics data from breast tumors were obtained by mass-spectrometry. Flux balance analysis was performed to study metabolic networks. Flux activities from metabolic pathways were calculated and used to build prognostic models. Results: Flux activities of vitamin A, tetrahydrobiopterin and β-alanine metabolism pathways split our population into low- and high-risk patients. Additionally, flux activities of glycolysis and glutamate metabolism split triple negative tumors into low- and high-risk groups. Conclusion: Flux activities summarize flux balance analysis data and can be associated with prognosis in cancer.
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Affiliation(s)
| | - Angelo Gámez-Pozo
- Biomedica Molecular Medicine SL, C/ Faraday 7, Madrid 28049, Spain.,Molecular Oncology & Pathology Lab, Institute of Medical & Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Paseo de la Castellana 261, Madrid 28046, Spain
| | - Mariana Díaz-Almirón
- Biostatistics Unit, La Paz University Hospital-IdiPAZ, Paseo de la Castellana 261, Madrid 28046, Spain
| | | | - Andrea Zapater-Moros
- Molecular Oncology & Pathology Lab, Institute of Medical & Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Paseo de la Castellana 261, Madrid 28046, Spain
| | - Rocío López-Vacas
- Molecular Oncology & Pathology Lab, Institute of Medical & Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Paseo de la Castellana 261, Madrid 28046, Spain
| | - Paolo Nanni
- Functional Genomics Centre Zurich, University of Zurich/ETH Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Pilar Zamora
- Medical Oncology Service, La Paz University Hospital-IdiPAZ, Paseo de la Castellana 261, Madrid 28046, Spain.,Cátedra UAM-Amgen, Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, Madrid 28049, Spain.,Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, C/ Melchor Fernández Almagro, 3, Madrid 28029, Spain
| | - Enrique Espinosa
- Medical Oncology Service, La Paz University Hospital-IdiPAZ, Paseo de la Castellana 261, Madrid 28046, Spain.,Cátedra UAM-Amgen, Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, Madrid 28049, Spain.,Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, C/ Melchor Fernández Almagro, 3, Madrid 28029, Spain
| | - Juan Ángel Fresno Vara
- Molecular Oncology & Pathology Lab, Institute of Medical & Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Paseo de la Castellana 261, Madrid 28046, Spain.,Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, C/ Melchor Fernández Almagro, 3, Madrid 28029, Spain
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Trilla-Fuertes L, Gámez-Pozo A, Prado-Vázquez G, Zapater-Moros A, Díaz-Almirón M, Arevalillo JM, Ferrer-Gómez M, Navarro H, Maín P, Espinosa E, Pinto Á, Vara JÁF. Biological molecular layer classification of muscle-invasive bladder cancer opens new treatment opportunities. BMC Cancer 2019; 19:636. [PMID: 31253132 PMCID: PMC6599340 DOI: 10.1186/s12885-019-5858-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 06/20/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Muscle-invasive bladder tumors are associated with a high risk of relapse and metastasis even after neoadjuvant chemotherapy and radical cystectomy. Therefore, further therapeutic options are needed and molecular characterization of the disease may help to identify new targets. The aim of this study was to characterize muscle-invasive bladder tumors at the molecular level using computational analyses. METHODS The TCGA cohort of muscle-invasive bladder cancer patients was used to describe these tumors. Probabilistic graphical models, layer analyses based on sparse k-means coupled with Consensus Cluster, and Flux Balance Analysis were applied to characterize muscle-invasive bladder tumors at a functional level. RESULTS Luminal and Basal groups were identified, and an immune molecular layer with independent value was also described. Luminal tumors showed decreased activity in the nodes of epidermis development and extracellular matrix, and increased activity in the node of steroid metabolism leading to a higher expression of the androgen receptor. This fact points to the androgen receptor as a therapeutic target in this group. Basal tumors were highly proliferative according to Flux Balance Analysis, which makes these tumors good candidates for neoadjuvant chemotherapy. The Immune-high group showed a higher degree of expression of immune biomarkers, suggesting that this group may benefit from immune therapy. CONCLUSIONS Our approach, based on layer analyses, established a Luminal group candidate for therapy with androgen receptor inhibitors, a proliferative Basal group which seems to be a good candidate for chemotherapy, and an immune-high group candidate for immunotherapy.
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Affiliation(s)
| | - Angelo Gámez-Pozo
- Biomedica Molecular Medicine SL, Madrid, Spain.,Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | | | - Andrea Zapater-Moros
- Biomedica Molecular Medicine SL, Madrid, Spain.,Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | | | - Jorge M Arevalillo
- Department of Statistics, Operational Research and Numerical Analysis, Universidad Nacional de Educación a Distancia (UNED), Madrid, Spain
| | - María Ferrer-Gómez
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Hilario Navarro
- Department of Statistics, Operational Research and Numerical Analysis, Universidad Nacional de Educación a Distancia (UNED), Madrid, Spain
| | - Paloma Maín
- Department of Statistics and Operations Research, Faculty of Mathematics, Complutense University of Madrid, Madrid, Spain
| | - Enrique Espinosa
- Servicio de Oncología Médica, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain.,Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
| | - Álvaro Pinto
- Servicio de Oncología Médica, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain.,Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain. .,Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain.
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Chiva C, Pastor O, Trilla-Fuertes L, Gámez-Pozo A, Fresno Vara JÁ, Sabidó E. Isotopologue Multipoint Calibration for Proteomics Biomarker Quantification in Clinical Practice. Anal Chem 2019; 91:4934-4938. [DOI: 10.1021/acs.analchem.8b05802] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Cristina Chiva
- Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Proteomics Unit, Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Olga Pastor
- Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Proteomics Unit, Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | | | - Angelo Gámez-Pozo
- Biomedica Molecular Medicine SL, C/Faraday 7, 28049, Madrid, Spain
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Eduard Sabidó
- Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Proteomics Unit, Universitat Pompeu Fabra, 08003, Barcelona, Spain
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Rojas L K, Trilla-Fuertes L, Gámez-Pozo A, Chiva C, Sepúlveda J, Manso L, Prado-Vázquez G, Zapater-Moros A, López-Vacas R, Ferrer-Gómez M, Mendiola C, Espinosa E, Sabidó E, Ciruelos E, Vara JÁF. Proteomics characterisation of central nervous system metastasis biomarkers in triple negative breast cancer. Ecancermedicalscience 2019; 13:891. [PMID: 30792808 PMCID: PMC6369972 DOI: 10.3332/ecancer.2019.891] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Indexed: 01/05/2023] Open
Abstract
Background Breast cancer (BC) is the most frequent tumour in women. Triple negative tumours (TNBC)-which are associated with minor survival rates-lack markers predictive of response to anticancer drugs. Triple negative tumours frequently metastasise to the central nervous system (CNS). Objective The main objective of this study was to study differences in tumour protein expression between patients with CNS metastases and those without this kind of spread, and propose new biomarkers. Methods A retrospective study was performed. Targeted proteomics and statistical analyses were used to identify possible biomarkers. Results Proteins were quantified by a targeted proteomics approach and protein expression data were successfully obtained from 51 triple negative formalin-fixed paraffin-embedded samples. ISG15, THBS1 and AP1M1 were identified as possible biomarkers related with CNS metastasis development. Conclusions Three possible biomarkers associated with CNS metastases in TNBC tumours were identified: ISG15, THBS1 and AP1M1. They may become markers predicting the appearance of CNS infiltration in triple negative BC.
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Affiliation(s)
- Katerin Rojas L
- Department of Medical Oncology, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain.,Katerin L Rojas and Lucía Trilla-Fuertes contributed equally to this work
| | - Lucía Trilla-Fuertes
- Biomedica Molecular Medicine SL, 28049 Madrid, Spain.,Katerin L Rojas and Lucía Trilla-Fuertes contributed equally to this work
| | - Angelo Gámez-Pozo
- Biomedica Molecular Medicine SL, 28049 Madrid, Spain.,Molecular Oncology and Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Hospital Universitario La Paz-IdiPAZ, 28029 Madrid, Spain
| | - Cristina Chiva
- Proteomics Unit, Center of Genomics Regulation, Barcelona Institute of Science and Technology, 08036 Barcelona, Spain.,Proteomics Unit, Universitat Pompeu Fabra, 08002 Barcelona, Spain
| | - Juan Sepúlveda
- Department of Medical Oncology, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Luis Manso
- Department of Medical Oncology, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Guillermo Prado-Vázquez
- Biomedica Molecular Medicine SL, 28049 Madrid, Spain.,Molecular Oncology and Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Hospital Universitario La Paz-IdiPAZ, 28029 Madrid, Spain
| | - Andrea Zapater-Moros
- Biomedica Molecular Medicine SL, 28049 Madrid, Spain.,Molecular Oncology and Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Hospital Universitario La Paz-IdiPAZ, 28029 Madrid, Spain
| | - Rocío López-Vacas
- Molecular Oncology and Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Hospital Universitario La Paz-IdiPAZ, 28029 Madrid, Spain
| | - María Ferrer-Gómez
- Molecular Oncology and Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Hospital Universitario La Paz-IdiPAZ, 28029 Madrid, Spain
| | - César Mendiola
- Department of Medical Oncology, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Enrique Espinosa
- Medical Oncology Service, Hospital Universitario La Paz-IdiPAZ, 28029 Madrid, Spain.,CIBERONC, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Eduard Sabidó
- Proteomics Unit, Center of Genomics Regulation, Barcelona Institute of Science and Technology, 08036 Barcelona, Spain.,Proteomics Unit, Universitat Pompeu Fabra, 08002 Barcelona, Spain
| | - Eva Ciruelos
- Department of Medical Oncology, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Juan Ángel Fresno Vara
- Biomedica Molecular Medicine SL, 28049 Madrid, Spain.,Molecular Oncology and Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Hospital Universitario La Paz-IdiPAZ, 28029 Madrid, Spain.,CIBERONC, Instituto de Salud Carlos III, 28029 Madrid, Spain
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Zapater-Moros A, Gámez-Pozo A, Prado-Vázquez G, Trilla-Fuertes L, Arevalillo JM, Díaz-Almirón M, Navarro H, Maín P, Feliú J, Zamora P, Espinosa E, Fresno Vara JÁ. Probabilistic graphical models relate immune status with response to neoadjuvant chemotherapy in breast cancer. Oncotarget 2018; 9:27586-27594. [PMID: 29963222 PMCID: PMC6021258 DOI: 10.18632/oncotarget.25496] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/08/2018] [Indexed: 12/28/2022] Open
Abstract
Breast cancer is the most frequent tumor in women and its incidence is increasing. Neoadjuvant chemotherapy has become standard of care as a complement to surgery in locally advanced or poor-prognosis early stage disease. The achievement of a complete response to neoadjuvant chemotherapy correlates with prognosis but it is not possible to predict who will obtain an excellent response. The molecular analysis of the tumor offers a unique opportunity to unveil predictive factors. In this work, gene expression profiling in 279 tumor samples from patients receiving neoadjuvant chemotherapy was performed and probabilistic graphical models were used. This approach enables addressing biological and clinical questions from a Systems Biology perspective, allowing to deal with large gene expression data and their interactions. Tumors presenting complete response to neoadjuvant chemotherapy had a higher activity of immune related functions compared to resistant tumors. Similarly, samples from complete responders presented higher expression of lymphocyte cell lineage markers, immune-activating and immune-suppressive markers, which may correlate with tumor infiltration by lymphocytes (TILs). These results suggest that the patient's immune system plays a key role in tumor response to neoadjuvant treatment. However, future studies with larger cohorts are necessary to validate these hypotheses.
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Affiliation(s)
- Andrea Zapater-Moros
- Molecular Oncology & Pathology Laboratory, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Angelo Gámez-Pozo
- Molecular Oncology & Pathology Laboratory, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
- Biomedica Molecular Medicine SL, Madrid, Spain
| | - Guillermo Prado-Vázquez
- Molecular Oncology & Pathology Laboratory, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | | | - Jorge M. Arevalillo
- Operational Research and Numerical Analysis, National Distance Education University, Madrid, Spain
| | | | - Hilario Navarro
- Operational Research and Numerical Analysis, National Distance Education University, Madrid, Spain
| | - Paloma Maín
- Department of Statistics and Operations Research, Faculty of Mathematics, Complutense University of Madrid, Madrid, Spain
| | - Jaime Feliú
- Medical Oncology Service, La Paz University Hospital-IdiPAZ, Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Pilar Zamora
- Medical Oncology Service, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Enrique Espinosa
- Medical Oncology Service, La Paz University Hospital-IdiPAZ, Madrid, Spain
- CIBERONC, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Molecular Oncology & Pathology Laboratory, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
- Biomedica Molecular Medicine SL, Madrid, Spain
- CIBERONC, Madrid, Spain
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Trilla-Fuertes L, Gámez-Pozo A, Arevalillo JM, Díaz-Almirón M, Prado-Vázquez G, Zapater-Moros A, Navarro H, Aras-López R, Dapía I, López-Vacas R, Nanni P, Llorente-Armijo S, Arias P, Borobia AM, Maín P, Feliú J, Espinosa E, Fresno Vara JÁ. Molecular characterization of breast cancer cell response to metabolic drugs. Oncotarget 2018. [PMID: 29515760 PMCID: PMC5839391 DOI: 10.18632/oncotarget.24047] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Metabolic reprogramming is a hallmark of cancer. It has been described that breast cancer subtypes present metabolism differences and this fact enables the possibility of using metabolic inhibitors as targeted drugs in specific scenarios. In this study, breast cancer cell lines were treated with metformin and rapamycin, showing a heterogeneous response to treatment and leading to cell cycle disruption. The genetic causes and molecular effects of this differential response were characterized by means of SNP genotyping and mass spectrometry-based proteomics. Protein expression was analyzed using probabilistic graphical models, showing that treatments elicit various responses in some biological processes such as transcription. Moreover, flux balance analysis using protein expression values showed that predicted growth rates were comparable with cell viability measurements and suggesting an increase in reactive oxygen species response enzymes due to metformin treatment. In addition, a method to assess flux differences in whole pathways was proposed. Our results show that these diverse approaches provide complementary information and allow us to suggest hypotheses about the response to drugs that target metabolism and their mechanisms of action.
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Affiliation(s)
- Lucía Trilla-Fuertes
- Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain.,Biomedica Molecular Medicine SL, Madrid, Spain
| | - Angelo Gámez-Pozo
- Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain.,Biomedica Molecular Medicine SL, Madrid, Spain
| | - Jorge M Arevalillo
- Operational Research and Numerical Analysis, National Distance Education University (UNED), Madrid, Spain
| | | | - Guillermo Prado-Vázquez
- Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Andrea Zapater-Moros
- Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Hilario Navarro
- Operational Research and Numerical Analysis, National Distance Education University (UNED), Madrid, Spain
| | - Rosa Aras-López
- Congenital Malformations Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital, IdiPAZ, Madrid, Spain
| | - Irene Dapía
- Pharmacogenetics Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Autonomous University of Madrid, Madrid, Spain.,Biomedical Research Networking Center on Rare Diseases-CIBERER, ISCIII, Madrid, Spain
| | - Rocío López-Vacas
- Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Paolo Nanni
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Sara Llorente-Armijo
- Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Pedro Arias
- Pharmacogenetics Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Autonomous University of Madrid, Madrid, Spain.,Biomedical Research Networking Center on Rare Diseases-CIBERER, ISCIII, Madrid, Spain
| | - Alberto M Borobia
- Clinical Pharmacology Department, La Paz University Hospital School of Medicine, IdiPAZ, Autonomous University of Madrid, Madrid, Spain
| | - Paloma Maín
- Department of Statistics and Operations Research, Faculty of Mathematics, Complutense University of Madrid, Madrid, Spain
| | - Jaime Feliú
- Medical Oncology Service, La Paz University Hospital-IdiPAZ, Madrid, Spain.,Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain.,Cátedra UAM-AMGEN, Universidad Autónoma de Madrid, Madrid, Spain
| | - Enrique Espinosa
- Medical Oncology Service, La Paz University Hospital-IdiPAZ, Madrid, Spain.,Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain.,Biomedica Molecular Medicine SL, Madrid, Spain.,Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
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Gámez-Pozo A, Trilla-Fuertes L, Prado-Vázquez G, Chiva C, López-Vacas R, Nanni P, Berges-Soria J, Grossmann J, Díaz-Almirón M, Ciruelos E, Sabidó E, Espinosa E, Fresno Vara JÁ. Prediction of adjuvant chemotherapy response in triple negative breast cancer with discovery and targeted proteomics. PLoS One 2017; 12:e0178296. [PMID: 28594844 PMCID: PMC5464546 DOI: 10.1371/journal.pone.0178296] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/10/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) accounts for 15-20% of all breast cancers and usually requires the administration of adjuvant chemotherapy after surgery but even with this treatment many patients still suffer from a relapse. The main objective of this study was to identify proteomics-based biomarkers that predict the response to standard adjuvant chemotherapy, so that patients at are not going to benefit from it can be offered therapeutic alternatives. METHODS We analyzed the proteome of a retrospective series of formalin-fixed, paraffin-embedded TNBC tissue applying high-throughput label-free quantitative proteomics. We identified several protein signatures with predictive value, which were validated with quantitative targeted proteomics in an independent cohort of patients and further evaluated in publicly available transcriptomics data. RESULTS Using univariate Cox analysis, a panel of 18 proteins was significantly associated with distant metastasis-free survival of patients (p<0.01). A reduced 5-protein profile with prognostic value was identified and its prediction performance was assessed in an independent targeted proteomics experiment and a publicly available transcriptomics dataset. Predictor P5 including peptides from proteins RAC2, RAB6A, BIEA and IPYR was the best performance protein combination in predicting relapse after adjuvant chemotherapy in TNBC patients. CONCLUSIONS This study identified a protein combination signature that complements histopathological prognostic factors in TNBC treated with adjuvant chemotherapy. The protein signature can be used in paraffin-embedded samples, and after a prospective validation in independent series, it could be used as predictive clinical test in order to recommend participation in clinical trials or a more exhaustive follow-up.
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Affiliation(s)
- Angelo Gámez-Pozo
- Molecular Oncology & Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
- Biomedica Molecular Medicine SL, Madrid, Spain
| | | | - Guillermo Prado-Vázquez
- Molecular Oncology & Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Cristina Chiva
- Proteomics Unit, Center of Genomics Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Proteomics Unit, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Rocío López-Vacas
- Molecular Oncology & Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Paolo Nanni
- Functional Genomics Centre Zurich, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Julia Berges-Soria
- Molecular Oncology & Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Jonas Grossmann
- Functional Genomics Centre Zurich, University of Zurich/ETH Zurich, Zurich, Switzerland
| | | | - Eva Ciruelos
- Medical Oncology Service, Instituto de Investigación Hospital Universitario Doce de Octubre-i+12, Madrid, Spain
| | - Eduard Sabidó
- Proteomics Unit, Center of Genomics Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Proteomics Unit, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Enrique Espinosa
- Medical Oncology Service, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
- CIBERONC. Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Molecular Oncology & Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
- Biomedica Molecular Medicine SL, Madrid, Spain
- CIBERONC. Instituto de Salud Carlos III, Madrid, Spain
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23
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Gámez-Pozo A, Berges-Soria J, Arevalillo JM, Nanni P, López-Vacas R, Navarro H, Grossmann J, Castaneda CA, Main P, Díaz-Almirón M, Espinosa E, Ciruelos E, Fresno Vara JÁ. Combined Label-Free Quantitative Proteomics and microRNA Expression Analysis of Breast Cancer Unravel Molecular Differences with Clinical Implications. Cancer Res 2015; 75:2243-53. [PMID: 25883093 DOI: 10.1158/0008-5472.can-14-1937] [Citation(s) in RCA: 49] [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: 07/03/2014] [Accepted: 03/12/2015] [Indexed: 11/16/2022]
Abstract
Better knowledge of the biology of breast cancer has allowed the use of new targeted therapies, leading to improved outcome. High-throughput technologies allow deepening into the molecular architecture of breast cancer, integrating different levels of information, which is important if it helps in making clinical decisions. microRNA (miRNA) and protein expression profiles were obtained from 71 estrogen receptor-positive (ER(+)) and 25 triple-negative breast cancer (TNBC) samples. RNA and proteins obtained from formalin-fixed, paraffin-embedded tumors were analyzed by RT-qPCR and LC/MS-MS, respectively. We applied probabilistic graphical models representing complex biologic systems as networks, confirming that ER(+) and TNBC subtypes are distinct biologic entities. The integration of miRNA and protein expression data unravels molecular processes that can be related to differences in the genesis and clinical evolution of these types of breast cancer. Our results confirm that TNBC has a unique metabolic profile that may be exploited for therapeutic intervention.
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Affiliation(s)
- Angelo Gámez-Pozo
- Molecular Oncology and Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Instituto de Investigación Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Julia Berges-Soria
- Molecular Oncology and Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Instituto de Investigación Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Jorge M Arevalillo
- Department of Statistics, Operational Research and Numerical Analysis, University Nacional Educacion a Distancia (UNED), Madrid, Spain
| | - Paolo Nanni
- Functional Genomics Centre Zurich, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Rocío López-Vacas
- Molecular Oncology and Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Instituto de Investigación Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Hilario Navarro
- Department of Statistics, Operational Research and Numerical Analysis, University Nacional Educacion a Distancia (UNED), Madrid, Spain
| | - Jonas Grossmann
- Functional Genomics Centre Zurich, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Carlos A Castaneda
- Departamento de Investigación, Instituto Nacional de Enfermedades Neoplásicas, Lima, Surquillo-Lima, Peru
| | - Paloma Main
- Department of Statistics and Operations Research, Faculty of Mathematics, Complutense University of Madrid, Madrid, Spain
| | - Mariana Díaz-Almirón
- Biostatistics Unit, Instituto de Investigación Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Enrique Espinosa
- Medical Oncology Service, Instituto de Investigación Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Eva Ciruelos
- Medical Oncology Service, Instituto de Investigación Hospital Universitario Doce de Octubre-i+12, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Molecular Oncology and Pathology Lab, Instituto de Genética Médica y Molecular-INGEMM, Instituto de Investigación Hospital Universitario La Paz-IdiPAZ, Madrid, Spain.
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24
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Gámez-Pozo A, Ferrer NI, Ciruelos E, López-Vacas R, Martínez FG, Espinosa E, Vara JÁF. Shotgun proteomics of archival triple-negative breast cancer samples. Proteomics Clin Appl 2013; 7:283-91. [DOI: 10.1002/prca.201200048] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 11/15/2012] [Accepted: 12/10/2012] [Indexed: 11/07/2022]
Affiliation(s)
- Angelo Gámez-Pozo
- Laboratorio de Oncología y Patología Molecular, Instituto de Genética Médica y Molecular-INGEMM; Instituto de Investigación Hospital Universitario La Paz-IdiPAZ; Madrid; Spain
| | - Nuria Ibarz Ferrer
- Unidad de Proteómica; Centro Nacional de Investigaciones Oncológicas (CNIO); Madrid; Spain
| | - Eva Ciruelos
- Servicio de Oncología; Instituto de Investigación Hospital Universitario Doce de Octubre-i+12; Madrid; Spain
| | - Rocío López-Vacas
- Laboratorio de Oncología y Patología Molecular, Instituto de Genética Médica y Molecular-INGEMM; Instituto de Investigación Hospital Universitario La Paz-IdiPAZ; Madrid; Spain
| | | | - Enrique Espinosa
- Servicio de Oncología Médica; Instituto de Investigación Hospital Universitario La Paz-IdiPAZ; Madrid; Spain
| | - Juan Ángel Fresno Vara
- Laboratorio de Oncología y Patología Molecular, Instituto de Genética Médica y Molecular-INGEMM; Instituto de Investigación Hospital Universitario La Paz-IdiPAZ; Madrid; Spain
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25
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Gámez‐Pozo A, Sánchez‐Navarro I, Ibarz Ferrer N, García Martínez F, Ashman K, Fresno Vara JÁ. High‐Throughput Phosphoproteomics from Formalin‐Fixed, Paraffin‐Embedded Tissues. ACTA ACUST UNITED AC 2012. [DOI: 10.1002/9780470559277.ch110242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Angelo Gámez‐Pozo
- Laboratorio de Oncología y Patología Molecular, Instituto de Genética Médica y Molecular‐INGEMM, Instituto de Investigación Hospital Universitario La Paz‐IdiPAZ Madrid Spain
| | - Iker Sánchez‐Navarro
- Laboratorio de Oncología y Patología Molecular, Instituto de Genética Médica y Molecular‐INGEMM, Instituto de Investigación Hospital Universitario La Paz‐IdiPAZ Madrid Spain
| | - Nuria Ibarz Ferrer
- Unidad de Proteómica, Centro Nacional de Investigaciones Oncológicas (CNIO) Madrid Spain
| | | | - Keith Ashman
- Unidad de Proteómica, Centro Nacional de Investigaciones Oncológicas (CNIO) Madrid Spain
- Clinical Applications Development, UQCCR University of Queensland Australia
| | - Juan Ángel Fresno Vara
- Laboratorio de Oncología y Patología Molecular, Instituto de Genética Médica y Molecular‐INGEMM, Instituto de Investigación Hospital Universitario La Paz‐IdiPAZ Madrid Spain
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26
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Gámez-Pozo A, Sánchez-Navarro I, Calvo E, Agulló-Ortuño MT, López-Vacas R, Díaz E, Camafeita E, Nistal M, Madero R, Espinosa E, López JA, Vara JÁF. PTRF/cavin-1 and MIF proteins are identified as non-small cell lung cancer biomarkers by label-free proteomics. PLoS One 2012; 7:e33752. [PMID: 22461895 PMCID: PMC3312891 DOI: 10.1371/journal.pone.0033752] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [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: 12/01/2011] [Accepted: 02/16/2012] [Indexed: 12/11/2022] Open
Abstract
With the completion of the human genome sequence, biomedical sciences have entered in the “omics” era, mainly due to high-throughput genomics techniques and the recent application of mass spectrometry to proteomics analyses. However, there is still a time lag between these technological advances and their application in the clinical setting. Our work is designed to build bridges between high-performance proteomics and clinical routine. Protein extracts were obtained from fresh frozen normal lung and non-small cell lung cancer samples. We applied a phosphopeptide enrichment followed by LC-MS/MS. Subsequent label-free quantification and bioinformatics analyses were performed. We assessed protein patterns on these samples, showing dozens of differential markers between normal and tumor tissue. Gene ontology and interactome analyses identified signaling pathways altered on tumor tissue. We have identified two proteins, PTRF/cavin-1 and MIF, which are differentially expressed between normal lung and non-small cell lung cancer. These potential biomarkers were validated using western blot and immunohistochemistry. The application of discovery-based proteomics analyses in clinical samples allowed us to identify new potential biomarkers and therapeutic targets in non-small cell lung cancer.
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Affiliation(s)
- Angelo Gámez-Pozo
- Laboratory of Molecular Pathology & Oncology, Instituto de Genética Médica y Molecular, Hospital Universitario La Paz, Madrid, Spain
| | - Iker Sánchez-Navarro
- Laboratory of Molecular Pathology & Oncology, Instituto de Genética Médica y Molecular, Hospital Universitario La Paz, Madrid, Spain
| | - Enrique Calvo
- Service of Proteomics, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | | | - Rocío López-Vacas
- Laboratory of Molecular Pathology & Oncology, Instituto de Genética Médica y Molecular, Hospital Universitario La Paz, Madrid, Spain
| | - Esther Díaz
- Laboratory of Molecular Pathology & Oncology, Instituto de Genética Médica y Molecular, Hospital Universitario La Paz, Madrid, Spain
| | - Emilio Camafeita
- Service of Proteomics, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Manuel Nistal
- Service of Pathology, Instituto de Investigación Sanitaria IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Rosario Madero
- Statistics Department, Instituto de Investigación Sanitaria IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Enrique Espinosa
- Service of Medical Oncology, Instituto de Investigación Sanitaria IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Juan Antonio López
- Service of Proteomics, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Laboratory of Molecular Pathology & Oncology, Instituto de Genética Médica y Molecular, Hospital Universitario La Paz, Madrid, Spain
- * E-mail:
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27
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Gámez-Pozo A, Sánchez-Navarro I, Calvo E, Díaz E, Miguel-Martín M, López R, Agulló T, Camafeita E, Espinosa E, López JA, Nistal M, Vara JÁF. Protein phosphorylation analysis in archival clinical cancer samples by shotgun and targeted proteomics approaches. Mol Biosyst 2011; 7:2368-74. [PMID: 21617801 DOI: 10.1039/c1mb05113j] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein phosphorylation affects most eukaryotic cellular processes and its deregulation is considered a hallmark of cancer and other diseases. Phosphoproteomics may enable monitoring of altered signaling pathways as a means of stratifying tumors and facilitating the discovery of new drugs. Unfortunately, the development of molecular tests for clinical use is constrained by the limited availability of fresh frozen, clinically annotated samples. Here we report phosphopeptide analysis in human archival formalin-fixed, paraffin-embedded (FFPE) cancer samples based on immobilized metal affinity chromatography followed by liquid chromatography coupled with tandem mass spectrometry and selected reaction monitoring techniques. Our results indicate the equivalence of detectable phosphorylation rates in archival FFPE and fresh frozen tissues. Moreover, we demonstrate the applicability of targeted assays for phosphopeptide analysis in clinical archival FFPE samples, using an experimental workflow suitable for processing and analyzing large sample series. This work paves the way for the application of shotgun and targeted phosphoproteomics approaches in clinically relevant studies using archival clinical samples.
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Affiliation(s)
- Angelo Gámez-Pozo
- Instituto de Investigación Sanitaria, IdIPAZ, Hospital Universitario La Paz, Madrid, Spain
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28
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Espinosa E, Vara JÁF, Navarro IS, Gámez-Pozo A, Pinto A, Zamora P, Redondo A, Feliu J. Gene profiling in breast cancer: time to move forward. Cancer Treat Rev 2011; 37:416-21. [PMID: 21277684 DOI: 10.1016/j.ctrv.2010.12.009] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 12/22/2010] [Accepted: 12/28/2010] [Indexed: 11/16/2022]
Abstract
Gene signatures may complement clinical and pathological factors to predict prognosis and response to therapy in patients with breast cancer, and can also sub-classify these tumours into entities with different biology and treatment requirements. A number of prognostic gene signatures are commercially available at this moment and two of them have entered phase III evaluation. Specific signatures are also being assessed to predict response to a number of drug therapies. The combined use of prognostic, predictive and subtype-defining signatures will guide therapeutic decisions in the future and will facilitate development of targeted drugs in specific groups of patients. However, cost-utility issues and some technical limitations have hindered widespread adoption of gene profiling. Gene signatures will become part of the routine clinical workup only if they help making clinical decisions. The first step to achieve this will consist of the inclusion of gene signatures in the design of clinical trials with new drugs.
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Affiliation(s)
- Enrique Espinosa
- Service of Oncology, Hospital La Paz & Instituto de Investigación Sanitaria IdiPAZ, Paseo de la Castellana, Madrid, Spain.
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29
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Gámez-Pozo A, Sánchez-Navarro I, Nistal M, Calvo E, Madero R, Díaz E, Camafeita E, de Castro J, López JA, González-Barón M, Espinosa E, Fresno Vara JÁ. MALDI profiling of human lung cancer subtypes. PLoS One 2009; 4:e7731. [PMID: 19890392 PMCID: PMC2767501 DOI: 10.1371/journal.pone.0007731] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [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: 07/03/2009] [Accepted: 10/08/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Proteomics is expected to play a key role in cancer biomarker discovery. Although it has become feasible to rapidly analyze proteins from crude cell extracts using mass spectrometry, complex sample composition hampers this type of measurement. Therefore, for effective proteome analysis, it becomes critical to enrich samples for the analytes of interest. Despite that one-third of the proteins in eukaryotic cells are thought to be phosphorylated at some point in their life cycle, only a low percentage of intracellular proteins is phosphorylated at a given time. METHODOLOGY/PRINCIPAL FINDINGS In this work, we have applied chromatographic phosphopeptide enrichment techniques to reduce the complexity of human clinical samples. A novel method for high-throughput peptide profiling of human tumor samples, using Parallel IMAC and MALDI-TOF MS, is described. We have applied this methodology to analyze human normal and cancer lung samples in the search for new biomarkers. Using a highly reproducible spectral processing algorithm to produce peptide mass profiles with minimal variability across the samples, lineal discriminant-based and decision tree-based classification models were generated. These models can distinguish normal from tumor samples, as well as differentiate the various non-small cell lung cancer histological subtypes. CONCLUSIONS/SIGNIFICANCE A novel, optimized sample preparation method and a careful data acquisition strategy is described for high-throughput peptide profiling of small amounts of human normal lung and lung cancer samples. We show that the appropriate combination of peptide expression values is able to discriminate normal lung from non-small cell lung cancer samples and among different histological subtypes. Our study does emphasize the great potential of proteomics in the molecular characterization of cancer.
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Affiliation(s)
- Angelo Gámez-Pozo
- Laboratory of Molecular Pathology and Oncology, Unidad de Investigación, Hospital Universitario La Paz, Madrid, Spain
| | - Iker Sánchez-Navarro
- Laboratory of Molecular Pathology and Oncology, Unidad de Investigación, Hospital Universitario La Paz, Madrid, Spain
| | - Manuel Nistal
- Laboratory of Molecular Pathology and Oncology, Unidad de Investigación, Hospital Universitario La Paz, Madrid, Spain
| | - Enrique Calvo
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Unidad de Proteómica, Madrid, Spain
| | - Rosario Madero
- Unidad de Bioestadística, Hospital Universitario La Paz, Madrid, Spain
| | - Esther Díaz
- Laboratory of Molecular Pathology and Oncology, Unidad de Investigación, Hospital Universitario La Paz, Madrid, Spain
| | - Emilio Camafeita
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Unidad de Proteómica, Madrid, Spain
| | - Javier de Castro
- Laboratory of Molecular Pathology and Oncology, Unidad de Investigación, Hospital Universitario La Paz, Madrid, Spain
| | - Juan Antonio López
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Unidad de Proteómica, Madrid, Spain
| | - Manuel González-Barón
- Laboratory of Molecular Pathology and Oncology, Unidad de Investigación, Hospital Universitario La Paz, Madrid, Spain
| | - Enrique Espinosa
- Laboratory of Molecular Pathology and Oncology, Unidad de Investigación, Hospital Universitario La Paz, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Laboratory of Molecular Pathology and Oncology, Unidad de Investigación, Hospital Universitario La Paz, Madrid, Spain
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Mendiola M, Barriuso J, Redondo A, Mariño-Enríquez A, Madero R, Espinosa E, Vara JÁF, Sánchez-Navarro I, Hernández-Cortes G, Zamora P, Pérez-Fernández E, Miguel-Martín M, Suárez A, Palacios J, González-Barón M, Hardisson D. Angiogenesis-related gene expression profile with independent prognostic value in advanced ovarian carcinoma. PLoS One 2008; 3:e4051. [PMID: 19112514 PMCID: PMC2605264 DOI: 10.1371/journal.pone.0004051] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [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: 11/10/2008] [Accepted: 11/24/2008] [Indexed: 12/20/2022] Open
Abstract
Background Ovarian carcinoma is the most important cause of gynecological cancer-related mortality in Western societies. Despite the improved median overall survival in patients receiving chemotherapy regimens such as paclitaxel and carboplatin combination, relapse still occurs in most advanced diseased patients. Increased angiogenesis is associated with rapid recurrence and decreased survival in ovarian cancer. This study was planned to identify an angiogenesis-related gene expression profile with prognostic value in advanced ovarian carcinoma patients. Methodology/Principal Findings RNAs were collected from formalin-fixed paraffin-embedded samples of 61 patients with III/IV FIGO stage ovarian cancer who underwent surgical cytoreduction and received a carboplatin plus paclitaxel regimen. Expression levels of 82 angiogenesis related genes were measured by quantitative real-time polymerase chain reaction using TaqMan low-density arrays. A 34-gene-profile which was able to predict the overall survival of ovarian carcinoma patients was identified. After a leave-one-out cross validation, the profile distinguished two groups of patients with different outcomes. Median overall survival and progression-free survival for the high risk group was 28.3 and 15.0 months, respectively, and was not reached by patients in the low risk group at the end of follow-up. Moreover, the profile maintained an independent prognostic value in the multivariate analysis. The hazard ratio for death was 2.3 (95% CI, 1.5 to 3.2; p<0.001). Conclusions/Significance It is possible to generate a prognostic model for advanced ovarian carcinoma based on angiogenesis-related genes using formalin-fixed paraffin-embedded samples. The present results are consistent with the increasing weight of angiogenesis genes in the prognosis of ovarian carcinoma.
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Affiliation(s)
- Marta Mendiola
- Department of Pathology, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain
- Fundación para la Investigación Biomédica del Hospital Universitario La Paz (FIBHULP), Madrid, Spain
| | - Jorge Barriuso
- Translational Oncology Unit, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain
- Fundación para la Investigación Biomédica del Hospital Universitario La Paz (FIBHULP), Madrid, Spain
| | - Andrés Redondo
- Translational Oncology Unit, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Adrián Mariño-Enríquez
- Department of Pathology, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Rosario Madero
- Unit of Biostatistics, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain
- Fundación para la Investigación Biomédica del Hospital Universitario La Paz (FIBHULP), Madrid, Spain
| | - Enrique Espinosa
- Translational Oncology Unit, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Fundación para la Investigación Biomédica del Hospital Universitario La Paz (FIBHULP), Madrid, Spain
| | - Iker Sánchez-Navarro
- Fundación para la Investigación Biomédica del Hospital Universitario La Paz (FIBHULP), Madrid, Spain
| | | | - Pilar Zamora
- Translational Oncology Unit, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Elia Pérez-Fernández
- Unit of Biostatistics, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain
- Fundación para la Investigación Biomédica del Hospital Universitario La Paz (FIBHULP), Madrid, Spain
| | - María Miguel-Martín
- Department of Pathology, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain
- Fundación para la Investigación Biomédica del Hospital Universitario La Paz (FIBHULP), Madrid, Spain
| | - Asunción Suárez
- Department of Pathology, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain
| | - José Palacios
- Department of Pathology, Hospital Universitario Vírgen del Rocío, Sevilla, Spain
| | - Manuel González-Barón
- Translational Oncology Unit, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain
| | - David Hardisson
- Department of Pathology, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain
- * E-mail:
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31
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Espinosa E, Vara JÁF, Redondo A, Sánchez JJ. In Reply:. J Clin Oncol 2005. [DOI: 10.1200/jco.2005.04.2382] [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: 11/20/2022] Open
Affiliation(s)
- Enrique Espinosa
- Service of Oncology, Hospital La Paz, Madrid, Department of Preventive Medicine, School of Medicine, Universidad Autónoma Madrid
| | - Juan Ángel Fresno Vara
- Service of Oncology, Hospital La Paz, Madrid, Department of Preventive Medicine, School of Medicine, Universidad Autónoma Madrid
| | - Andrés Redondo
- Service of Oncology, Hospital La Paz, Madrid, Department of Preventive Medicine, School of Medicine, Universidad Autónoma Madrid
| | - José Javier Sánchez
- Service of Oncology, Hospital La Paz, Madrid, Department of Preventive Medicine, School of Medicine, Universidad Autónoma Madrid
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