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Medina-Medina R, Iglesias-Flores E, Benítez JM, Marín-Pedrosa S, Salgueiro-Rodríguez I, Linares CI, González-Rubio S, Soto-Escribano P, Gros B, Rodríguez-Perálvarez ML, Cabriada JL, Chaparro M, Gisbert JP, Chicano-Gálvez E, Ortea I, Ferrín G, García-Sánchez V, Aguilar-Melero P. Development of a Prediction Model for Short-Term Remission of Patients with Crohn's Disease Treated with Anti-TNF Drugs. Int J Mol Sci 2023; 24:ijms24108695. [PMID: 37240037 DOI: 10.3390/ijms24108695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Therapy with anti-tumor necrosis factor (TNF) has dramatically changed the natural history of Crohn's disease (CD). However, these drugs are not without adverse events, and up to 40% of patients could lose efficacy in the long term. We aimed to identify reliable markers of response to anti-TNF drugs in patients with CD. A consecutive cohort of 113 anti-TNF naive patients with CD was stratified according to clinical response as short-term remission (STR) or non-STR (NSTR) at 12 weeks of treatment. We compared the protein expression profiles of plasma samples in a subset of patients from both groups prior to anti-TNF therapy by SWATH proteomics. We identified 18 differentially expressed proteins (p ≤ 0.01, fold change ≥ 2.4) involved in the organization of the cytoskeleton and cell junction, hemostasis/platelet function, carbohydrate metabolism, and immune response as candidate biomarkers of STR. Among them, vinculin was one of the most deregulated proteins (p < 0.001), whose differential expression was confirmed by ELISA (p = 0.054). In the multivariate analysis, plasma vinculin levels along with basal CD Activity Index, corticosteroids induction, and bowel resection were factors predicting NSTR.
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Affiliation(s)
- Rosario Medina-Medina
- Gastroenterology Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba, 14004 Córdoba, Spain
| | - Eva Iglesias-Flores
- Gastroenterology Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba, 14004 Córdoba, Spain
| | - Jose M Benítez
- Gastroenterology Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba, 14004 Córdoba, Spain
| | - Sandra Marín-Pedrosa
- Gastroenterology Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba, 14004 Córdoba, Spain
| | - Isabel Salgueiro-Rodríguez
- Gastroenterology Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba, 14004 Córdoba, Spain
| | - Clara I Linares
- Gastroenterology Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba, 14004 Córdoba, Spain
| | - Sandra González-Rubio
- Gastroenterology Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba, 14004 Córdoba, Spain
| | - Pilar Soto-Escribano
- Gastroenterology Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba, 14004 Córdoba, Spain
| | - Beatriz Gros
- Gastroenterology Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba, 14004 Córdoba, Spain
| | - Manuel L Rodríguez-Perálvarez
- Gastroenterology Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba, 14004 Córdoba, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - José L Cabriada
- Gastroenterology Unit, Hospital Universitario de Galdakao, 48960 Galdakao, Spain
| | - María Chaparro
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, 28006 Madrid, Spain
| | - Javier P Gisbert
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, 28006 Madrid, Spain
| | - Eduardo Chicano-Gálvez
- Proteomics Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba, 14004 Córdoba, Spain
| | - Ignacio Ortea
- Proteomics Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba, 14004 Córdoba, Spain
| | - Gustavo Ferrín
- Gastroenterology Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba, 14004 Córdoba, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Valle García-Sánchez
- Gastroenterology Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba, 14004 Córdoba, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Patricia Aguilar-Melero
- Gastroenterology Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba, 14004 Córdoba, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
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Abstract
Classical and culture-based methods for the identification and characterization of the biochemical properties of microorganisms are slow and labor-intensive. Liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) has been used for the analysis of bacterial pathogen strain-specific diagnostic peptides allowing the characterization of bacterial strains.Here, we describe the analysis of tryptic digestion peptides by LC-ESI-MS/MS to search for specific biomarkers useful for the rapid identification of, on the one hand, the bacterial species and, on the other hand, the physiological and biochemical characteristics such as the expression of virulence factors, including toxins, immune-modulatory factors, and exoenzymes.
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Affiliation(s)
- Ana G Abril
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Campus Sur 15782, Universidad de Santiago de Compostela, A Coruña, Spain
| | - Ignacio Ortea
- Institute Maimónides of Biomedica Investigation of Córdoba, Córdoba, Spain
| | - Jorge Barros-Velázquez
- Departamento de Química Analítica, Nutrición y Bromatología, Area de Tecnología de los Alimentos, Facultad de Veterinaria, Campus Lugo, 27002, Universidad de Santiago de Compostela, A Coruña, Spain
| | - Tomás G Villa
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Campus Sur 15782, Universidad de Santiago de Compostela, A Coruña, Spain
| | - Pilar Calo-Mata
- Departamento de Química Analítica, Nutrición y Bromatología, Area de Tecnología de los Alimentos, Facultad de Veterinaria, Campus Lugo, 27002, Universidad de Santiago de Compostela, A Coruña, Spain.
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González-Fernández MJ, Ortea I, Guil-Guerrero JL. α-Linolenic and γ-linolenic acids exercise differential antitumor effects on HT-29 human colorectal cancer cells. Toxicol Res (Camb) 2020; 9:474-483. [PMID: 32905142 DOI: 10.1093/toxres/tfaa046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/30/2020] [Accepted: 06/03/2020] [Indexed: 12/19/2022] Open
Abstract
α-Linolenic acid (ALA, 18:3n-3) and γ-gamma linolenic acid (GLA, 18:3n-6) are polyunsaturated fatty acids (PUFA) that improve the human health. The present study focused on testing the in vitro antitumor actions of pure ALA and GLA on the HT-29 human colorectal cancer cell line. Cell viability was checked by MTT ((3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) test, cell membrane damage by the lactate dehydrogenase assay, apoptosis was tested by both caspase-3 activity trial and transmission electron microscopy images, and protein composition was analyzed by quantitative proteomics analysis. MTT test revealed IC50 values of 230 and 255 μM for ALA and GLA, respectively, at 72 h. After 24 h of incubation, both ALA and GLA induced apoptosis on HT-29 colorectal cancer cells according to the caspase-3 assay and microscopy images. SWATH/MS analysis evidenced that ALA significantly affected the mitochondrial protein import pathway and the citric acid cycle pathway, while GLA did not significantly affect any particular pathway. In summary, both ALA and GLA showed concentration-dependent inhibitory effects on HT-29 cells viability and induced cell death by apoptosis. ALA significantly affected cellular pathways, while GLA does not have specific actions on either pathway. Both n-3 and n-6 C18 PUFA are bioactive food components useful in the colorectal cancer prevention.
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Affiliation(s)
- María José González-Fernández
- Food Technology Division, Agrifood Campus of International Excellence, ceiA3, University of Almería, E-040120 Almería, Spain
| | - Ignacio Ortea
- Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz 11009, Spain
| | - José Luis Guil-Guerrero
- Food Technology Division, Agrifood Campus of International Excellence, ceiA3, University of Almería, E-040120 Almería, Spain
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Bock JO, Ortea I. Re-analysis of SARS-CoV-2-infected host cell proteomics time-course data by impact pathway analysis and network analysis: a potential link with inflammatory response. Aging (Albany NY) 2020; 12:11277-11286. [PMID: 32575076 PMCID: PMC7343490 DOI: 10.18632/aging.103524] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/30/2020] [Indexed: 12/11/2022]
Abstract
Coronavirus disease 2019 (COVID-19), caused by an outbreak of the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) in Wuhan, China, has led to an unprecedented health and economic crisis worldwide. To develop treatments that can stop or lessen the symptoms and severity of SARS-CoV-2 infection, it is critical to understand how the virus behaves inside human cells, and so far studies in this area remain scarce. A recent study investigated translatome and proteome host cell changes induced in vitro by SARS-CoV-2. Here, we use the publicly available proteomics data from this study to re-analyze the in vitro cellular consequences of SARS-CoV-2 infection by impact pathways analysis and network analysis. Notably, proteins linked to the inflammatory response, but also proteins related to chromosome segregation during mitosis, were found to be altered in response to viral infection. Upregulation of inflammatory response proteins is in line with the propagation of inflammatory reaction and lung injury that is observed in advanced stages of COVID-19 patients and which worsens with age.
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Affiliation(s)
| | - Ignacio Ortea
- Proteomics Unit, Universidad de Cádiz and Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz 11002, Spain
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González-Fernández MJ, Fabrikov D, Ramos-Bueno RP, Guil-Guerrero JL, Ortea I. SWATH Differential Abundance Proteomics and Cellular Assays Show In Vitro Anticancer Activity of Arachidonic Acid- and Docosahexaenoic Acid-Based Monoacylglycerols in HT-29 Colorectal Cancer Cells. Nutrients 2019; 11:E2984. [PMID: 31817645 PMCID: PMC6950369 DOI: 10.3390/nu11122984] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/02/2019] [Accepted: 12/04/2019] [Indexed: 12/20/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common and mortal types of cancer. There is increasing evidence that some polyunsaturated fatty acids (PUFAs) exercise specific inhibitory actions on cancer cells through different mechanisms, as a previous study on CRC cells demonstrated for two very long-chain PUFA. These were docosahexaenoic acid (DHA, 22:6n3) and arachidonic acid (ARA, 20:4n6) in the free fatty acid (FFA) form. In this work, similar design and technology have been used to investigate the actions of both DHA and ARA as monoacylglycerol (MAG) molecules, and results have been compared with those obtained using the corresponding FFA. Cell assays revealed that ARA- and DHA-MAG exercised dose- and time-dependent antiproliferative actions, with DHA-MAG acting on cancer cells more efficiently than ARA-MAG. Sequential window acquisition of all theoretical mass spectra (SWATH) - mass spectrometry massive quantitative proteomics, validated by parallel reaction monitoring and followed by pathway analysis, revealed that DHA-MAG had a massive effect in the proteasome complex, while the ARA-MAG main effect was related to DNA replication. Prostaglandin synthesis also resulted as inhibited by DHA-MAG. Results clearly demonstrated the ability of both ARA- and DHA-MAG to induce cell death in colon cancer cells, which suggests a direct relationship between chemical structure and antitumoral actions.
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Affiliation(s)
- María José González-Fernández
- Food Technology Division, Agrifood Campus of International Excellence, ceiA3, University of Almería, 40120 Almería, Spain; (M.J.G.-F.); (D.F.); (R.P.R.-B.); (J.L.G.-G.)
| | - Dmitri Fabrikov
- Food Technology Division, Agrifood Campus of International Excellence, ceiA3, University of Almería, 40120 Almería, Spain; (M.J.G.-F.); (D.F.); (R.P.R.-B.); (J.L.G.-G.)
| | - Rebeca P. Ramos-Bueno
- Food Technology Division, Agrifood Campus of International Excellence, ceiA3, University of Almería, 40120 Almería, Spain; (M.J.G.-F.); (D.F.); (R.P.R.-B.); (J.L.G.-G.)
| | - José Luis Guil-Guerrero
- Food Technology Division, Agrifood Campus of International Excellence, ceiA3, University of Almería, 40120 Almería, Spain; (M.J.G.-F.); (D.F.); (R.P.R.-B.); (J.L.G.-G.)
| | - Ignacio Ortea
- Proteomics Unit, IMIBIC, Reina Sofía University Hospital, University of Córdoba, 14004 Córdoba, Spain
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López-Sánchez LM, Jiménez-Izquierdo R, Peñarando J, Mena R, Guil-Luna S, Toledano M, Conde F, Villar C, Díaz C, Ortea I, De la Haba-Rodríguez JR, Aranda E, Rodríguez-Ariza A. SWATH-based proteomics reveals processes associated with immune evasion and metastasis in poor prognosis colorectal tumours. J Cell Mol Med 2019; 23:8219-8232. [PMID: 31560832 PMCID: PMC6850959 DOI: 10.1111/jcmm.14693] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/25/2019] [Accepted: 08/25/2019] [Indexed: 01/02/2023] Open
Abstract
Newly emerged proteomic methodologies, particularly data‐independent acquisition (DIA) analysis–related approaches, would improve current gene expression–based classifications of colorectal cancer (CRC). Therefore, this study was aimed to identify protein expression signatures using SWATH‐MS DIA and targeted data extraction, to aid in the classification of molecular subtypes of CRC and advance in the diagnosis and development of new drugs. For this purpose, 40 human CRC samples and 7 samples of healthy tissue were subjected to proteomic and bioinformatic analysis. The proteomic analysis identified three different molecular CRC subtypes: P1, P2 and P3. Significantly, P3 subtype showed high agreement with the mesenchymal/stem‐like subtype defined by gene expression signatures and characterized by poor prognosis and survival. The P3 subtype was characterized by decreased expression of ribosomal proteins, the spliceosome, and histone deacetylase 2, as well as increased expression of osteopontin, SERPINA 1 and SERPINA 3, and proteins involved in wound healing, acute inflammation and complement pathway. This was also confirmed by immunodetection and gene expression analyses. Our results show that these tumours are characterized by altered expression of proteins involved in biological processes associated with immune evasion and metastasis, suggesting new therapeutic options in the treatment of this aggressive type of CRC.
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Affiliation(s)
- Laura M López-Sánchez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Jon Peñarando
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Rafael Mena
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Silvia Guil-Luna
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Marta Toledano
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Francisco Conde
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Carlos Villar
- Unidad de Gestión Clínica de Anatomía Patológica, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - César Díaz
- Unidad de Gestión Clínica de Cirugía General y del Aparato Digestivo, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Ignacio Ortea
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Juan R De la Haba-Rodríguez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Unidad de Gestión Clínica de Oncología Médica, Hospital Universitario Reina Sofía, Universidad de Córdoba, Córdoba, Spain
| | - Enrique Aranda
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Unidad de Gestión Clínica de Oncología Médica, Hospital Universitario Reina Sofía, Universidad de Córdoba, Córdoba, Spain
| | - Antonio Rodríguez-Ariza
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Unidad de Gestión Clínica de Oncología Médica, Hospital Universitario Reina Sofía, Universidad de Córdoba, Córdoba, Spain
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Abstract
Adulteration and mislabeling of food products and the commercial fraud derived, either intentionally or not, is a global source of economic fraud to consumers but also to all stakeholders involved in food production and distribution. Legislation has been enforced all over the world aimed at guaranteeing the authenticity of the food products all along the distribution chain, thereby avoiding food fraud and adulteration. Accordingly, there is a growing need for new analytical methods able to verify that all the ingredients included in a foodstuff match the qualities claimed by the manufacturer or distributor. In this sense, the improved performance of most recent DNA-based tools in term of sensitivity, multiplexing ability, high-throughput, and relatively low-cost give them a game-changing role in food-authenticity-related topics. Here, we provide a thorough and updated vision on the recently reported approaches that are applying these DNA-based tools to assess the authenticity of food components and products.
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Affiliation(s)
- Karola Böhme
- Department of Analytical Chemistry, Nutrition and Food Science , University of Santiago de Compostela , E-27002 Lugo , Spain
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science , University of Santiago de Compostela , E-27002 Lugo , Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science , University of Santiago de Compostela , E-27002 Lugo , Spain
| | - Ignacio Ortea
- Proteomics Unit , Maimonides Institute for Biomedical Research (IMIBIC) , E-14004 Córdoba , Spain
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Fernandez AF, Bayón GF, Sierra MI, Urdinguio RG, Toraño EG, García MG, Carella A, López V, Santamarina P, Pérez RF, Belmonte T, Tejedor JR, Cobo I, Menendez P, Mangas C, Ferrero C, Rodrigo L, Astudillo A, Ortea I, Cueto Díaz S, Rodríguez-Gonzalez P, García Alonso JI, Mollejo M, Meléndez B, Domínguez G, Bonilla F, Fraga MF. Loss of 5hmC identifies a new type of aberrant DNA hypermethylation in glioma. Hum Mol Genet 2019; 27:3046-3059. [PMID: 29878202 DOI: 10.1093/hmg/ddy214] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 05/29/2018] [Indexed: 01/13/2023] Open
Abstract
Aberrant DNA hypermethylation is a hallmark of cancer although the underlying molecular mechanisms are still poorly understood. To study the possible role of 5-hydroxymethylcytosine (5hmC) in this process we analyzed the global and locus-specific genome-wide levels of 5hmC and 5-methylcytosine (5mC) in human primary samples from 12 non-tumoral brains and 53 gliomas. We found that the levels of 5hmC identified in non-tumoral samples were significantly reduced in gliomas. Strikingly, hypo-hydroxymethylation at 4627 (9.3%) CpG sites was associated with aberrant DNA hypermethylation and was strongly enriched in CpG island shores. The DNA regions containing these CpG sites were enriched in H3K4me2 and presented a different genuine chromatin signature to that characteristic of the genes classically aberrantly hypermethylated in cancer. As this 5mC gain is inversely correlated with loss of 5hmC and has not been identified with classical sodium bisulfite-based technologies, we conclude that our data identifies a novel 5hmC-dependent type of aberrant DNA hypermethylation in glioma.
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Affiliation(s)
| | | | | | - Rocio G Urdinguio
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Principado de Asturias, Oviedo, Spain
| | - Estela G Toraño
- Institute of Oncology of Asturias (IUOPA), ISPA-HUCA.,Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Principado de Asturias, Oviedo, Spain
| | - Maria G García
- Institute of Oncology of Asturias (IUOPA), ISPA-HUCA.,Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Principado de Asturias, Oviedo, Spain
| | - Antonella Carella
- Institute of Oncology of Asturias (IUOPA), ISPA-HUCA.,Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Principado de Asturias, Oviedo, Spain
| | - Virginia López
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Principado de Asturias, Oviedo, Spain
| | - Pablo Santamarina
- Institute of Oncology of Asturias (IUOPA), ISPA-HUCA.,Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Principado de Asturias, Oviedo, Spain
| | - Raúl F Pérez
- Institute of Oncology of Asturias (IUOPA), ISPA-HUCA.,Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Principado de Asturias, Oviedo, Spain
| | - Thalía Belmonte
- Institute of Oncology of Asturias (IUOPA), ISPA-HUCA.,Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Principado de Asturias, Oviedo, Spain
| | | | - Isabel Cobo
- Institute of Oncology of Asturias (IUOPA), ISPA-HUCA.,Department of Biomedicine, School of Medicine, Josep Carreras Leukemia Research Institute, University of Barcelona, Barcelona, Spain
| | - Pablo Menendez
- Department of Biomedicine, School of Medicine, Josep Carreras Leukemia Research Institute, University of Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Centro de Investigacion Biomedica en Red en Cancer CIBER-ONC, ISCIII, Barcelona, Spain
| | | | | | - Luis Rodrigo
- Department of Gastroenterology, Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Aurora Astudillo
- Department of Pathology, Instituto Universitario de Oncología del Principado de Asturias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Ignacio Ortea
- Proteomics Unit, IMIBIC, Maimonides Institute for Biomedical Research, Córdoba, Spain
| | | | | | | | - Manuela Mollejo
- Department of Pathology, Hospital Virgen de la Salud, Avd. Barber 30, Toledo 45005, Spain
| | - Bárbara Meléndez
- Department of Pathology, Hospital Virgen de la Salud, Avd. Barber 30, Toledo 45005, Spain
| | - Gemma Domínguez
- Servicio de Oncología Médica, Hospital Universitario Puerta de Hierro, Majadahonda, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Felix Bonilla
- Servicio de Oncología Médica, Hospital Universitario Puerta de Hierro, Majadahonda, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Mario F Fraga
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Principado de Asturias, Oviedo, Spain
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Böhme K, Calo-Mata P, Barros-Velázquez J, Ortea I. Recent applications of omics-based technologies to main topics in food authentication. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.11.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Ortea I, González-Fernández MJ, Ramos-Bueno RP, Guil-Guerrero JL. Proteomics Study Reveals That Docosahexaenoic and Arachidonic Acids Exert Different In Vitro Anticancer Activities in Colorectal Cancer Cells. J Agric Food Chem 2018; 66:6003-6012. [PMID: 29804451 DOI: 10.1021/acs.jafc.8b00915] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Two polyunsaturated fatty acids, docosahexaenoic acid (DHA) and arachidonic acid (ARA), as well as derivatives, such as eicosanoids, regulate different activities, affecting transcription factors and, therefore, DNA transcription, being a critical step for the functioning of fatty-acid-derived signaling. This work has attempted to determine the in vitro anticancer activities of these molecules linked to the gene transcription regulation of HT-29 colorectal cancer cells. We applied the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide test along with lactate dehydrogenase and caspase-3 assays; proteome changes were assessed by "sequential windowed acquisition of all theoretical mass spectra" quantitative proteomics, followed by pathway analysis, to determine the affected molecular mechanisms. In all assays, DHA inhibited cell proliferation of HT-29 cells to a higher extent than ARA and acted primarily by downregulating proteasome particles, while ARA presented a dramatic effect on all six DNA replication helicase particles. The results indicated that both DHA and ARA are potential chemopreventive agent candidates.
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Affiliation(s)
- Ignacio Ortea
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía , Universidad de Córdoba , E14004 Córdoba , Spain
| | - María José González-Fernández
- Food Technology Division, Agrifood Campus of International Excellence (ceiA3) , University of Almería , E40120 Almería , Spain
| | - Rebeca P Ramos-Bueno
- Food Technology Division, Agrifood Campus of International Excellence (ceiA3) , University of Almería , E40120 Almería , Spain
| | - José Luis Guil-Guerrero
- Food Technology Division, Agrifood Campus of International Excellence (ceiA3) , University of Almería , E40120 Almería , Spain
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12
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Ortea I, Ruiz-Sánchez I, Cañete R, Caballero-Villarraso J, Cañete MD. Identification of candidate serum biomarkers of childhood-onset growth hormone deficiency using SWATH-MS and feature selection. J Proteomics 2018; 175:105-113. [PMID: 29317355 DOI: 10.1016/j.jprot.2018.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/30/2017] [Accepted: 01/04/2018] [Indexed: 12/13/2022]
Abstract
A typical clinical manifestation of growth hormone deficiency (GHD) is a short stature resulting from delayed growth, but GHD affects bone health, cardiovascular function and metabolic profile and therefore quality of life. Although early GH treatment during childhood has been shown to improve outcomes, no single biochemical parameter is currently available for the accurate diagnosis of GHD in children. There is hence a need for non-invasive biomarkers. In this study, the relative abundance of serum proteins from GHD children and healthy controls was measured by next-generation proteomics SWATH-MS technology. The data generated was analysed by machine-learning feature-selection algorithms in order to discover the minimum number of protein biomarkers that best discriminate between both groups. The analysis of serum proteins by a SWATH-MS approach yielded a useful method for discovering potential biomarkers of GHD in children. A total of 263 proteins were confidently detected and quantified in each sample. Pathway analysis indicated an effect on tissue/organ structure and morphogenesis. The top ten serum protein biomarker candidates were identified after applying feature-selection data analysis. The combination of three proteins - apolipoprotein A-IV, complement factor H-related protein 4 and platelet basic protein - demonstrated the best classification performance for our data. In addition, the apolipoprotein group resulted in strong over-representation, thus highlighting these proteins as an additional promising biomarker panel. SIGNIFICANCE Currently there is no single biochemical parameter available for the accurate diagnosis of growth hormone (GH) deficiency (GHD) in children. Simple GH measurements are not an option: because GH is released in a pulsatile action, its blood levels fluctuate throughout the day and remain nearly undetectable for most of that time. This makes measurements of GH in a single blood sample useless for assessing GH deficiency. Actually, the diagnosis of GHD includes a combination of direct and indirect non-accurate measurements, such as taking several body measurements, testing GH levels in multiple blood samples after provocative tests (GH peak <7.3ng/mL, using radioimmunoassay), and conducting magnetic resonance imaging (MRI), among others. Therefore, there is a need for simple, non-invasive, accurate and cost-effective biomarkers. Here we report a case-control study, where relative abundance of serum proteins were measured by next-generation proteomics SWATH-MS technology in 15 GHD children and 15healthy controls matched by age, sex, and not receiving any treatment. Data generated was analysed by machine learning feature selection algorithms. 263 proteins could be confidently detected and quantified on each sample. The top 10 serum protein biomarker candidates could be identified after applying a feature selection data analysis. The combination of three proteins, apolipoprotein A-IV, complement factor H-related protein 4 and platelet basic protein, showed the best classification performance for our data. In addition, the fact that the pathway and GO analysis we performed pointed to the apolipoproteins as over-represented highlights this protein group as an additional promising biomarker panel for the diagnosis of GHD and for treatment evaluation.
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Affiliation(s)
- Ignacio Ortea
- Proteomics Unit, IMIBIC, Hospital Universitario Reina Sofía, Universidad de Córdoba, Cordoba, Spain.
| | | | - Ramón Cañete
- Universidad de Córdoba, Córdoba, Spain; GA-05, IMIBIC, Córdoba, Spain
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Vialas V, Colomé-Calls N, Abian J, Aloria K, Alvarez-Llamas G, Antúnez O, Arizmendi JM, Azkargorta M, Barceló-Batllori S, Barderas MG, Blanco F, Casal JI, Casas V, de la Torre C, Chicano-Gálvez E, Elortza F, Espadas G, Estanyol JM, Fernandez-Irigoyen J, Fernandez-Puente P, Fidalgo MJ, Fuentes M, Gay M, Gil C, Hainard A, Hernaez ML, Ibarrola N, Kopylov AT, Lario A, Lopez JA, López-Lucendo M, Marcilla M, Marina-Ramírez A, Marko-Varga G, Martín L, Mora MI, Morato-López E, Muñoz J, Odena MA, de Oliveira E, Orera I, Ortea I, Pasquarello C, Ray KB, Rezeli M, Ruppen I, Sabidó E, Del Pino MMS, Sancho J, Santamaría E, Vazquez J, Vilaseca M, Vivanco F, Walters JJ, Zgoda VG, Corrales FJ, Canals F, Paradela A. A multicentric study to evaluate the use of relative retention times in targeted proteomics. J Proteomics 2016; 152:138-149. [PMID: 27989941 DOI: 10.1016/j.jprot.2016.10.014] [Citation(s) in RCA: 8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/27/2016] [Accepted: 10/24/2016] [Indexed: 12/19/2022]
Abstract
Despite the maturity reached by targeted proteomic strategies, reliable and standardized protocols are urgently needed to enhance reproducibility among different laboratories and analytical platforms, facilitating a more widespread use in biomedical research. To achieve this goal, the use of dimensionless relative retention times (iRT), defined on the basis of peptide standard retention times (RT), has lately emerged as a powerful tool. The robustness, reproducibility and utility of this strategy were examined for the first time in a multicentric setting, involving 28 laboratories that included 24 of the Spanish network of proteomics laboratories (ProteoRed-ISCIII). According to the results obtained in this study, dimensionless retention time values (iRTs) demonstrated to be a useful tool for transferring and sharing peptide retention times across different chromatographic set-ups both intra- and inter-laboratories. iRT values also showed very low variability over long time periods. Furthermore, parallel quantitative analyses showed a high reproducibility despite the variety of experimental strategies used, either MRM (multiple reaction monitoring) or pseudoMRM, and the diversity of analytical platforms employed. BIOLOGICAL SIGNIFICANCE From the very beginning of proteomics as an analytical science there has been a growing interest in developing standardized methods and experimental procedures in order to ensure the highest quality and reproducibility of the results. In this regard, the recent (2012) introduction of the dimensionless retention time concept has been a significant advance. In our multicentric (28 laboratories) study we explore the usefulness of this concept in the context of a targeted proteomics experiment, demonstrating that dimensionless retention time values is a useful tool for transferring and sharing peptide retention times across different chromatographic set-ups.
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Affiliation(s)
- Vital Vialas
- ProteoRed-ISCIII, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Núria Colomé-Calls
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain
| | - Joaquín Abian
- ProteoRed-ISCIII, Instituto de Investigaciones Biomédicas de Barcelona, IIBB-CSIC/IDIBAPS, Barcelona 08036, Spain
| | - Kerman Aloria
- Department of Biochemistry and Molecular Biology, University of the Basque Country-UPV/EHU, Leioa 48940, Spain
| | | | - Oreto Antúnez
- ProteoRed-ISCIII, SCSIE Universitat de Valencia, Burjassot 46100, Spain
| | - Jesus M Arizmendi
- ProteoRed-ISCIII, University of the Basque Country-UPV/EHU, Leioa 48940, Spain
| | - Mikel Azkargorta
- ProteoRed-ISCIII, CIC bioGUNE, Science and Technology Park of Bizkaia, Derio, Spain
| | | | - María G Barderas
- ProteoRed-ISCIII, Hospital Nacional de Parapléjicos-SESCAM, Toledo, Spain
| | | | - J Ignacio Casal
- ProteoRed-ISCIII, Centro de Investigaciones Biológicas-CSIC, Madrid 28040, Spain
| | - Vanessa Casas
- ProteoRed-ISCIII, Instituto de Investigaciones Biomédicas de Barcelona, IIBB-CSIC/IDIBAPS, Barcelona 08036, Spain
| | - Carolina de la Torre
- ProteoRed-ISCIII, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Eduardo Chicano-Gálvez
- ProteoRed-ISCIII, Maimonides Institute for Biomedical Research and Universidad de Córdoba, Córdoba 14004, Spain
| | - Felix Elortza
- ProteoRed-ISCIII, CIC bioGUNE, Science and Technology Park of Bizkaia, Derio, Spain
| | - Guadalupe Espadas
- ProteoRed-ISCIII, Centre de Regulació Genòmica, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Josep M Estanyol
- ProteoRed-ISCIII, Scientific and Technological Centers (CCiTUB), University of Barcelona, Barcelona 08036, Spain
| | | | | | - María José Fidalgo
- ProteoRed-ISCIII, Scientific and Technological Centers (CCiTUB), University of Barcelona, Barcelona 08036, Spain
| | - Manuel Fuentes
- ProteoRed-ISCIII, Cancer Research Center, University of Salamanca-CSIC, IBSAL, Salamanca 37007, Spain
| | - Marina Gay
- ProteoRed-ISCIII, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain
| | - Concha Gil
- ProteoRed-ISCIII, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Alexandre Hainard
- Proteomics Core Facility CMU, University of Geneva, Geneva, Switzerland
| | | | - Nieves Ibarrola
- ProteoRed-ISCIII, Cancer Research Center, University of Salamanca-CSIC, IBSAL, Salamanca 37007, Spain
| | - Arthur T Kopylov
- Orekhovich Institute of Biomedical Chemistry RAMS, Moscow 119121, Russian Federation
| | - Antonio Lario
- ProteoRed-ISCIII, IPBLN (CSIC), Armilla, Granada, Spain
| | - Juan Antonio Lopez
- ProteoRed-ISCIII, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - María López-Lucendo
- ProteoRed-ISCIII, Centro de Investigaciones Biológicas-CSIC, Madrid 28040, Spain
| | - Miguel Marcilla
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), Madrid 28049, Spain
| | | | - Gyorgy Marko-Varga
- Centre of Excellence in Biological and Medical Mass spectrometry, Lund University, Lund, Sweden
| | - Luna Martín
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain
| | - Maria I Mora
- ProteoRed-ISCIII, CIMA, University of Navarra, Pamplona 31008, Spain
| | | | - Javier Muñoz
- ProteoRed-ISCIII, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | | | | | - Irene Orera
- ProteoRed-ISCIII, Instituto Aragonés de Ciencias de la Salud, Zaragoza 50009, Spain
| | - Ignacio Ortea
- ProteoRed-ISCIII, Maimonides Institute for Biomedical Research and Universidad de Córdoba, Córdoba 14004, Spain
| | - Carla Pasquarello
- Proteomics Core Facility CMU, University of Geneva, Geneva, Switzerland
| | | | - Melinda Rezeli
- Centre of Excellence in Biological and Medical Mass spectrometry, Lund University, Lund, Sweden
| | - Isabel Ruppen
- ProteoRed-ISCIII, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Eduard Sabidó
- ProteoRed-ISCIII, Centre de Regulació Genòmica, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | | | - Jaime Sancho
- ProteoRed-ISCIII, IPBLN (CSIC), Armilla, Granada, Spain
| | - Enrique Santamaría
- ProteoRed-ISCIII, Navarrabiomed Biomedical Research Center-IdiSNa, Pamplona, Spain
| | - Jesus Vazquez
- ProteoRed-ISCIII, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Marta Vilaseca
- ProteoRed-ISCIII, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain
| | | | | | - Victor G Zgoda
- Orekhovich Institute of Biomedical Chemistry RAMS, Moscow 119121, Russian Federation
| | | | - Francesc Canals
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain.
| | - Alberto Paradela
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), Madrid 28049, Spain.
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Ortea I, Roschitzki B, López-Rodríguez R, Tomero EG, Ovalles JG, López-Longo J, de la Torre I, González-Alvaro I, Gómez-Reino JJ, González A. Independent Candidate Serum Protein Biomarkers of Response to Adalimumab and to Infliximab in Rheumatoid Arthritis: An Exploratory Study. PLoS One 2016; 11:e0153140. [PMID: 27050469 PMCID: PMC4822871 DOI: 10.1371/journal.pone.0153140] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 11/16/2015] [Accepted: 03/24/2016] [Indexed: 12/19/2022] Open
Abstract
Response to treatment of rheumatoid arthritis shows large inter-individual variability. This heterogeneity is observed with all the anti-rheumatic drugs, including the commonly used TNF inhibitors. It seems that drug-specific and target-specific factors lead individual patients to respond or not to a given drug, although this point has been challenged. The search of biomarkers distinguishing responders from non-responders has included shotgun proteomics of serum, as a previous study of response to infliximab, an anti-TNF antibody. Here, we have used the same study design and technology to search biomarkers of response to a different anti-TNF antibody, adalimumab, and we have compared the results obtained for the two anti-TNF drugs. Search of biomarkers of response to adalimumab included depletion of the most abundant serum proteins, 8-plex isobaric tag for relative and absolute quantitation (iTRAQ) labeling, two-dimensional liquid chromatography fractionation and relative quantification with a hybrid Orbitrap mass spectrometer. With this approach, 264 proteins were identified in all the samples with at least 2 peptides and 95% confidence. Nine proteins showed differences between non-responders and responders (P < 0.05), representing putative biomarkers of response to adalimumab. These results were compared with the previous study of infliximab. Surprisingly, the non-responder/responder differences in the two studies were not correlated (rs = 0.07; P = 0.40). This overall independence with all the proteins showed two identifiable components. On one side, the putative biomarkers of response to either adalimumab or infliximab, which were not shared and showed an inverse correlation (rs = -0.69; P = 0.0023). On the other, eight proteins showing significant non-responder/responder differences in the analysis combining data of response to the two drugs. These results identify new putative biomarkers of response to treatment of rheumatoid arthritis and indicate that they are notably drug-specific.
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Affiliation(s)
- Ignacio Ortea
- Laboratorio Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
| | - Bernd Roschitzki
- Functional Genomics Center Zurich, University and ETH Zurich, Switzerland
| | - Rosario López-Rodríguez
- Laboratorio Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
| | - Eva G. Tomero
- Rheumatology Unit, Hospital Universitario de La Princesa, Instituto Investigacion Sanitaria Princesa, Madrid, Spain
| | - Juan G. Ovalles
- Rheumatology Unit, Hospital General Universitario Gregorio Marañon, Madrid, Spain
| | - Javier López-Longo
- Rheumatology Unit, Hospital General Universitario Gregorio Marañon, Madrid, Spain
| | | | - Isidoro González-Alvaro
- Rheumatology Unit, Hospital Universitario de La Princesa, Instituto Investigacion Sanitaria Princesa, Madrid, Spain
| | - Juan J. Gómez-Reino
- Laboratorio Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
- Department of Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio González
- Laboratorio Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria - Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
- * E-mail:
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Ortea I, Rodríguez-Ariza A, Chicano-Gálvez E, Arenas Vacas MS, Jurado Gámez B. Discovery of potential protein biomarkers of lung adenocarcinoma in bronchoalveolar lavage fluid by SWATH MS data-independent acquisition and targeted data extraction. J Proteomics 2016; 138:106-14. [PMID: 26917472 DOI: 10.1016/j.jprot.2016.02.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/01/2016] [Accepted: 02/13/2016] [Indexed: 12/11/2022]
Abstract
UNLABELLED Lung cancer currently ranks as the neoplasia with the highest global mortality rate. Although some improvements have been introduced in recent years, new advances in diagnosis are required in order to increase survival rates. New mildly invasive endoscopy-based diagnostic techniques include the collection of bronchoalveolar lavage fluid (BALF), which is discarded after using a portion of the fluid for standard pathological procedures. BALF proteomic analysis can contribute to clinical practice with more sensitive biomarkers, and can complement cytohistological studies by aiding in the diagnosis, prognosis, and subtyping of lung cancer, as well as the monitoring of treatment response. The range of quantitative proteomics methodologies used for biomarker discovery is currently being broadened with the introduction of data-independent acquisition (DIA) analysis-related approaches that address the massive quantitation of the components of a proteome. Here we report for the first time a DIA-based quantitative proteomics study using BALF as the source for the discovery of potential lung cancer biomarkers. The results have been encouraging in terms of the number of identified and quantified proteins. A panel of candidate protein biomarkers for adenocarcinoma in BALF is reported; this points to the activation of the complement network as being strongly over-represented and suggests this pathway as a potential target for lung cancer research. In addition, the results reported for haptoglobin, complement C4-A, and glutathione S-transferase pi are consistent with previous studies, which indicates that these proteins deserve further consideration as potential lung cancer biomarkers in BALF. Our study demonstrates that the analysis of BALF proteins by liquid chromatography-tandem mass spectrometry (LC-MS/MS), combining a simple sample pre-treatment and SWATH DIA MS, is a useful method for the discovery of potential lung cancer biomarkers. SIGNIFICANCE Bronchoalveolar lavage fluid (BALF) analysis can contribute to clinical practice with more sensitive biomarkers, thus complementing cytohistological studies in order to aid in the diagnosis, prognosis, and subtyping of lung cancer, as well as the monitoring of treatment response. Here we report a panel of candidate protein biomarkers for adenocarcinoma in BALF. Forty-four proteins showed a fold-change higher than 3.75 among adenocarcinoma patients compared with controls. This report is the first DIA-based quantitative proteomics study to use bronchoalveolar lavage fluid (BALF) as a matrix for discovering potential biomarkers. The results are encouraging in terms of the number of identified and quantified proteins, demonstrating that the analysis of BALF proteins by a SWATH approach is a useful method for the discovery of potential biomarkers of pulmonary diseases.
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Affiliation(s)
- I Ortea
- Proteomics Unit, IMIBIC, Maimonides Institute for Biomedical Research, Córdoba, Spain.
| | - A Rodríguez-Ariza
- Medical Oncology Department, Reina Sofia University Hospital and IMIBIC, Maimonides Institute for Biomedical Research, Córdoba, Spain
| | - E Chicano-Gálvez
- Proteomics Unit, IMIBIC, Maimonides Institute for Biomedical Research, Córdoba, Spain
| | - M S Arenas Vacas
- Department of Respiratory Medicine, Reina Sofia University Hospital and IMIBIC, Maimonides Institute for Biomedical Research, Córdoba, Spain
| | - B Jurado Gámez
- Department of Respiratory Medicine, Reina Sofia University Hospital and IMIBIC, Maimonides Institute for Biomedical Research, Córdoba, Spain
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de Andres MC, Perez-Pampin E, Calaza M, Santaclara FJ, Ortea I, Gomez-Reino JJ, Gonzalez A. Assessment of global DNA methylation in peripheral blood cell subpopulations of early rheumatoid arthritis before and after methotrexate. Arthritis Res Ther 2015; 17:233. [PMID: 26330155 PMCID: PMC4556005 DOI: 10.1186/s13075-015-0748-5] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [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: 01/31/2015] [Accepted: 08/10/2015] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION DNA methylation is an epigenetic mechanism regulating gene expression that has been insufficiently studied in the blood of rheumatoid arthritis (RA) patients, as only T cells and total peripheral blood mononuclear cells (PBMCs) from patients with established RA have been studied and with conflicting results. METHOD Five major blood cell subpopulations: T, B and NK cells, monocytes, and polymorphonuclear leukocytes, were isolated from 19 early RA patients and 17 healthy controls. Patient samples were taken before and 1 month after the start of treatment with methotrexate (MTX). Analysis included DNA methylation with high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry-selected reaction monitoring (HPLC-ESI-MS/MS-SRM) and expression levels of seven methylation-specific enzymes by quantitative polymerase chain reaction (qPCR). RESULTS Disease-modifying anti-rheumatic drug (DMARD)-naïve early RA patients showed global DNA hypomethylation in T cells and monocytes, together with a lower expression of DNA methyltrasnferase 1 (DNMT1), the maintenance DNA methyltransferase, which was also decreased in B cells. Furthermore, significantly increased expression of ten-eleven translocation1 (TET1), TET2 and TET3, enzymes involved in demethylation, was found in monocytes and of TET2 in T cells. There was also modest decreased expression of DNMT3A in B cells and of growth arrest and DNA-damage-inducible protein 45A (GADD45A) in T and B cells. Treatment with MTX reverted hypomethylation in T cells and monocytes, which were no longer different from controls, and increased global methylation in B cells. In addition, DNMT1 and DNMT3A showed a trend to reversion of their decreased expression. CONCLUSIONS Our results confirm global DNA hypomethylation in patients with RA with specificity for some blood cell subpopulations and their reversal with methotrexate treatment. These changes are accompanied by parallel changes in the levels of enzymes involved in methylation, suggesting the possibility of regulation at this level.
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Affiliation(s)
- María C de Andres
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigación Sanitaria-Hospital Clínico Universitario de Santiago, Travesia de Choupana, s/n, 15706, Santiago de Compostela, Spain.
| | - Eva Perez-Pampin
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigación Sanitaria-Hospital Clínico Universitario de Santiago, Travesia de Choupana, s/n, 15706, Santiago de Compostela, Spain.
| | - Manuel Calaza
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigación Sanitaria-Hospital Clínico Universitario de Santiago, Travesia de Choupana, s/n, 15706, Santiago de Compostela, Spain.
| | - Francisco J Santaclara
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigación Sanitaria-Hospital Clínico Universitario de Santiago, Travesia de Choupana, s/n, 15706, Santiago de Compostela, Spain.
| | - Ignacio Ortea
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigación Sanitaria-Hospital Clínico Universitario de Santiago, Travesia de Choupana, s/n, 15706, Santiago de Compostela, Spain.
| | - Juan J Gomez-Reino
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigación Sanitaria-Hospital Clínico Universitario de Santiago, Travesia de Choupana, s/n, 15706, Santiago de Compostela, Spain.
- Department of Medicine, University of Santiago de Compostela, Rúa de San Francisco, s/n, 15782, Santiago de Compostela, Spain.
| | - Antonio Gonzalez
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigación Sanitaria-Hospital Clínico Universitario de Santiago, Travesia de Choupana, s/n, 15706, Santiago de Compostela, Spain.
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Prado M, Ortea I, Vial S, Rivas J, Calo-Mata P, Barros-Velázquez J. Advanced DNA- and Protein-based Methods for the Detection and Investigation of Food Allergens. Crit Rev Food Sci Nutr 2015; 56:2511-2542. [DOI: 10.1080/10408398.2013.873767] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Ortea I, Gallardo JM. Investigation of production method, geographical origin and species authentication in commercially relevant shrimps using stable isotope ratio and/or multi-element analyses combined with chemometrics: An exploratory analysis. Food Chem 2015; 170:145-53. [DOI: 10.1016/j.foodchem.2014.08.049] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 06/24/2014] [Accepted: 08/11/2014] [Indexed: 10/24/2022]
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de Andrés MC, Perez-Pampin E, Calaza M, Ortea I, Gomez-Reino JJ, Gonzalez A. THU0021 DNA Methylation of Peripheral Blood Cell Subpopulations in Patients with Early Rheumatoid Arthritis before and after Methotrexate Treatment. Ann Rheum Dis 2013. [DOI: 10.1136/annrheumdis-2013-eular.549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Ortea I, Roschitzki B, Ovalles J, Lopez-Longo F, de la Torre I, Gonzalez I, Gomez-Reino J, Gonzalez A. AB0290 Serum protein biomarkers for response of rheumatoid arthritis to infliximab. Ann Rheum Dis 2013. [DOI: 10.1136/annrheumdis-2012-eular.290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Ortea I, Roschitzki B, Ovalles JG, Longo JL, de la Torre I, González I, Gómez-Reino JJ, González A. Discovery of serum proteomic biomarkers for prediction of response to infliximab (a monoclonal anti-TNF antibody) treatment in rheumatoid arthritis: An exploratory analysis. J Proteomics 2012; 77:372-82. [DOI: 10.1016/j.jprot.2012.09.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 09/07/2012] [Accepted: 09/11/2012] [Indexed: 12/22/2022]
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Ortea I, Pascoal A, Cañas B, Gallardo JM, Barros-Velázquez J, Calo-Mata P. Food authentication of commercially-relevant shrimp and prawn species: From classical methods to Foodomics. Electrophoresis 2012; 33:2201-11. [DOI: 10.1002/elps.201100576] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ignacio Ortea
- Department of Food Technology; Institute for Marine Research; Spanish National Research Council (CSIC); Vigo; Spain
| | - Ananías Pascoal
- Department of Analytical Chemistry; Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology; University of Santiago de Compostela; Lugo; Spain
| | - Benito Cañas
- Department of Analytical Chemistry; University Complutense of Madrid; Madrid; Spain
| | - José M. Gallardo
- Department of Food Technology; Institute for Marine Research; Spanish National Research Council (CSIC); Vigo; Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry; Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology; University of Santiago de Compostela; Lugo; Spain
| | - Pilar Calo-Mata
- Department of Analytical Chemistry; Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology; University of Santiago de Compostela; Lugo; Spain
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Pascoal A, Ortea I, Gallardo JM, Cañas B, Barros-Velázquez J, Calo-Mata P. Species identification of the Northern shrimp (Pandalus borealis) by polymerase chain reaction-restriction fragment length polymorphism and proteomic analysis. Anal Biochem 2011; 421:56-67. [PMID: 22080038 DOI: 10.1016/j.ab.2011.10.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 10/15/2011] [Accepted: 10/17/2011] [Indexed: 10/16/2022]
Abstract
Genomic and proteomic techniques for species identification of meat and seafood products are being widely used. In this study, a genomic approach was used to differentiate Pandalus borealis (the Northern shrimp), which belongs to the superfamily Pandaloidea, from 30 crustaceans consisting of 19 commercially relevant prawns/shrimps species that belong to the superfamily Penaeoidea, which include the families Penaeidae and Solenoceridae, and 11 other crustacean species, including prawns, shrimps, lobsters, and crabs. For this purpose, a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was designed based on the amplification of the 16S rRNA/tRNA(Val)/12S rRNA mitochondrial regions using the primers 16S-CruF and 16S-CruR. The 966-bp PCR products were produced and cleaved with the restriction enzymes AluI, TaqI, and HinfI, which provided species-specific restriction patterns. In addition, a proteomic approach, based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and electrospray ionization-ion trap (ESI-IT) mass spectrometry, was used to identify and characterize new P. borealis-specific peptides that could be useful as potential markers of this species in protein-based detection methods. To our knowledge, this is the first time a molecular method has been successfully applied to identify a wide range of prawn and shrimp species, including P. borealis, for either whole individuals or processed products. However, validation of the methods proposed here is required by applying them to a larger sample of individuals from different populations and geographic origins in order to avoid mainly false-negative results.
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Affiliation(s)
- Ananias Pascoal
- Department of Analytical Chemistry, Nutrition, and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, E-27002 Lugo, Spain
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Ortea I, Cañas B, Gallardo JM. Selected tandem mass spectrometry ion monitoring for the fast identification of seafood species. J Chromatogr A 2011; 1218:4445-51. [PMID: 21621784 DOI: 10.1016/j.chroma.2011.05.032] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 02/22/2011] [Accepted: 05/09/2011] [Indexed: 11/16/2022]
Abstract
Selected tandem mass spectrometry (MS/MS) ion monitoring (SMIM) is the most suitable scanning mode to detect known peptides in complex samples when an ion-trap mass spectrometer is the instrument used for the analysis. In this mode, the MS detector is programmed to perform continuous MS/MS scans on one or more selected precursors, either during a selected time interval, or along the whole chromatographic run. MS/MS spectra are recorded, so virtual multiple reaction monitoring chromatogram traces for the different fragment ions can be plotted. In this work, a shotgun proteomics approach was applied to the detection of previously characterized species-specific peptides from different seafood species. The proposed methodology makes use of high intensity focused ultrasound-assisted trypsin digestion for ultra fast sample preparation, peptide separation and identification by reverse phase capillary LC coupled to an ion-trap working in the SMIM scanning mode. This methodology was applied to the differential classification of seven commercial, closely related, species of Decapoda shrimps proving to be an excellent tool for seafood product authentication, which may be used by fisheries and manufacturers to provide a fast and effective identification of the specimens, guaranteeing the quality and safety of foodstuffs to consumers.
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Affiliation(s)
- Ignacio Ortea
- Marine Research Institute, Spanish National Research Council (CSIC), Vigo, Spain.
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Ortea I, Cañas B, Gallardo JM. Mass spectrometry characterization of species-specific peptides from arginine kinase for the identification of commercially relevant shrimp species. J Proteome Res 2010; 8:5356-62. [PMID: 19891510 DOI: 10.1021/pr900663d] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The identification of commercial shrimp species is a relevant issue to ensure correct labeling, maintain consumer confidence and enhance the knowledge of the captured species, benefiting both, fisheries and manufacturers. A proteomic approach, based on 2DE, tryptic in-gel digestion, MALDI-TOF MS, and ESI-MS/MS analyses, is proposed for the identification of shrimp species with commercial interest. MALDI-TOF peptide mass fingerprint from arginine kinase tryptic digests were used for the identification of seven commercial, closely related species of Decapoda shrimps. Further identification and characterization of these peptides was performed by CID on an ESI-IT instrument, database search and de novo sequence interpretation, paying special attention to differential, species-specific peptides. Fisheries and manufacturers may take advantage of this methodology as a tool for a rapid and effective seafood product identification and authentication, providing and guaranteeing the quality and safety of the foodstuffs to consumers.
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Affiliation(s)
- Ignacio Ortea
- Marine Research Institute, Spanish National Research Council (CSIC), Eduardo Cabello 6, E-36208 Vigo, Spain.
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Ortea I, Cañas B, Calo-Mata P, Barros-Velázquez J, Gallardo JM. Arginine kinase peptide mass fingerprinting as a proteomic approach for species identification and taxonomic analysis of commercially relevant shrimp species. J Agric Food Chem 2009; 57:5665-5672. [PMID: 19489608 DOI: 10.1021/jf900520h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A proteomic approach aimed at species identification and taxonomic analysis of shrimp species of commercial interest is presented. Six different species belonging to the order Decapoda were considered. Preliminary, two-dimensional gel electrophoresis (2-DE) analysis of the sarcoplasmic proteome revealed interspecific variability in the isoelectric point (pI) of arginine kinase. For this reason, arginine kinase spot was selected as a potential molecular marker and subjected to tryptic digestion followed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) peptide mass fingerprinting (PMF) analysis. Arginine kinase PMF allowed the differentiation of the six species studied. Four samples of commercial origin obtained in local markets were analyzed to validate the methodology. The PMF cluster analysis also provided information about the phylogenetic relationships in these species. The application of this methodology may be of interest for the differentiation and taxonomic analysis of shrimp species complementing DNA-based phylogenetic studies.
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Affiliation(s)
- Ignacio Ortea
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas, Vigo, Spain.
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Ortea I, Barros L, Gallardo JM. Closely Related Shrimp Species Identification by MALDI-ToF Mass Spectrometry. Journal of Aquatic Food Product Technology 2009. [DOI: 10.1080/10498850802584280] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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