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Viasus D, Nonell L, Restrepo C, Figueroa F, Donado-Mazarrón C, Carratalà J. A Systematic Review of Gene Expression Studies in Critically Ill Patients with Sepsis and Community-Acquired Pneumonia. Biomedicines 2023; 11:2755. [PMID: 37893128 PMCID: PMC10604146 DOI: 10.3390/biomedicines11102755] [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: 08/17/2023] [Revised: 09/14/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
(1) Background: Sepsis is present in nearly 90% of critically ill patients with community-acquired pneumonia (CAP). This systematic review updates the information on studies that have assessed gene expression profiles in critically ill septic patients with CAP. (2) Methods: We searched for studies that satisfied the following criteria: (a) expression profile in critically ill patients with sepsis due to CAP, (b) presence of a control group, and (c) adult patients. Over-representation analysis was performed with clusterProfiler using the Hallmark and Reactome collections. (3) Results: A total of 4312 differentially expressed genes (DEGs) and sRNAs were included in the enrichment analysis. In the Hallmark collection, genes regulated by nuclear factor kappa B in response to tumor necrosis factor, genes upregulated by signal transducer and activator of transcription 5 in response to interleukin 2 stimulation, genes upregulated in response to interferon-gamma, genes defining the inflammatory response, a subgroup of genes regulated by MYC-version 1 (v1), and genes upregulated during transplant rejection were significantly enriched in critically ill septic patients with CAP. Moreover, 88 pathways were identified in the Reactome database. (4) Conclusions: This study summarizes the reported DEGs in critically ill septic patients with CAP and investigates their functional implications. The results highlight the complexity of immune responses during CAP.
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Affiliation(s)
- Diego Viasus
- Department of Medicine, Division of Health Sciences, Universidad del Norte and Hospital Universidad del Norte, Barranquilla 081001, Colombia
| | - Lara Nonell
- Departament de Biociències, Universitat de Vic—Universitat Central de Catalunya, 08500 Barcelona, Spain;
| | - Carlos Restrepo
- Department of Medicine, Division of Health Sciences, Universidad del Norte and Hospital Universidad del Norte, Barranquilla 081001, Colombia
| | - Fabian Figueroa
- Department of Medicine, Division of Health Sciences, Universidad del Norte and Hospital Universidad del Norte, Barranquilla 081001, Colombia
| | - Carla Donado-Mazarrón
- Department of Infectious Diseases, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona, 08907 Barcelona, Spain;
| | - Jordi Carratalà
- Department of Infectious Diseases, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona, 08907 Barcelona, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
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2
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Pujals M, Mayans C, Bellio C, Méndez O, Greco E, Fasani R, Alemany-Chavarria M, Zamora E, Padilla L, Mitjans F, Nuciforo P, Canals F, Nonell L, Abad M, Saura C, Tabernero J, Villanueva J. RAGE/SNAIL1 signaling drives epithelial-mesenchymal plasticity in metastatic triple-negative breast cancer. Oncogene 2023; 42:2610-2628. [PMID: 37468678 DOI: 10.1038/s41388-023-02778-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/29/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023]
Abstract
Epithelial/Mesenchymal (E/M) plasticity plays a fundamental role both in embryogenesis and during tumorigenesis. The receptor for advanced glycation end products (RAGE) is a driver of cell plasticity in fibrotic diseases; however, its role and molecular mechanism in triple-negative breast cancer (TNBC) remains unclear. Here, we demonstrate that RAGE signaling maintains the mesenchymal phenotype of aggressive TNBC cells by enforcing the expression of SNAIL1. Besides, we uncover a crosstalk mechanism between the TGF-β and RAGE pathways that is required for the acquisition of mesenchymal traits in TNBC cells. Consistently, RAGE inhibition elicits epithelial features that block migration and invasion capacities. Next, since RAGE is a sensor of the tumor microenvironment, we modeled acute acidosis in TNBC cells and showed it promotes enhanced production of RAGE ligands and the activation of RAGE-dependent invasive properties. Furthermore, acute acidosis increases SNAIL1 levels and tumor cell invasion in a RAGE-dependent manner. Finally, we demonstrate that in vivo inhibition of RAGE reduces metastasis incidence and expands survival, consistent with molecular effects that support the relevance of RAGE signaling in E/M plasticity. These results uncover new molecular insights on the regulation of E/M phenotypes in cancer metastasis and provide rationale for pharmacological intervention of this signaling axis.
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Affiliation(s)
- Mireia Pujals
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carla Mayans
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - Chiara Bellio
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Olga Méndez
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Emanuela Greco
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Roberta Fasani
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Mercè Alemany-Chavarria
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Esther Zamora
- Medical Oncology Service, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Laura Padilla
- LEITAT Technological Center, 08028, Barcelona, Spain
| | | | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Francesc Canals
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Lara Nonell
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - María Abad
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Altos Labs Cambridge Institute of Science, Cambridge, UK
| | - Cristina Saura
- Medical Oncology Service, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Josep Tabernero
- Medical Oncology Service, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- IOB Institute of Oncology, Quiron Group (Quiron-IOB), Barcelona, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Villanueva
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain.
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3
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Rombauts A, Bódalo Torruella M, Abelenda-Alonso G, Perera-Bel J, Ferrer-Salvador A, Acedo-Terrades A, Gabarrós-Subirà M, Oriol I, Gudiol C, Nonell L, Carratalà J. Dynamics of Gene Expression Profiling and Identification of High-Risk Patients for Severe COVID-19. Biomedicines 2023; 11:biomedicines11051348. [PMID: 37239019 DOI: 10.3390/biomedicines11051348] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 04/03/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/28/2023] Open
Abstract
The clinical manifestations of SARS-CoV-2 infection vary widely, from asymptomatic infection to the development of acute respiratory distress syndrome (ARDS) and death. The host response elicited by SARS-CoV-2 plays a key role in determining the clinical outcome. We hypothesized that determining the dynamic whole blood transcriptomic profile of hospitalized adult COVID-19 patients and characterizing the subgroup that develops severe disease and ARDS would broaden our understanding of the heterogeneity in clinical outcomes. We recruited 60 hospitalized patients with RT-PCR-confirmed SARS-CoV-2 infection, among whom 19 developed ARDS. Peripheral blood was collected using PAXGene RNA tubes within 24 h of admission and on day 7. There were 2572 differently expressed genes in patients with ARDS at baseline and 1149 at day 7. We found a dysregulated inflammatory response in COVID-19 ARDS patients, with an increased expression of genes related to pro-inflammatory molecules and neutrophil and macrophage activation at admission, in addition to an immune regulation loss. This led, in turn, to a higher expression of genes related to reactive oxygen species, protein polyubiquitination, and metalloproteinases in the latter stages. Some of the most significant differences in gene expression found between patients with and without ARDS corresponded to long non-coding RNA involved in epigenetic control.
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Affiliation(s)
- Alexander Rombauts
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | | | - Gabriela Abelenda-Alonso
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | - Júlia Perera-Bel
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Anna Ferrer-Salvador
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | | | - Maria Gabarrós-Subirà
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Isabel Oriol
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | - Carlota Gudiol
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
- Department of Medicine, Universitat de Barcelona, 08007 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Lara Nonell
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Jordi Carratalà
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
- Department of Medicine, Universitat de Barcelona, 08007 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
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4
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Zacarías-Fluck MF, Massó-Vallés D, Giuntini F, González-Larreategui Í, Kaur J, Casacuberta-Serra S, Jauset T, Martínez-Martín S, Martín-Fernández G, Serrano Del Pozo E, Foradada L, Grueso J, Nonell L, Beaulieu ME, Whitfield JR, Soucek L. Reducing MYC's transcriptional footprint unveils a good prognostic gene signature in melanoma. Genes Dev 2023; 37:303-320. [PMID: 37024284 PMCID: PMC10153459 DOI: 10.1101/gad.350078.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 03/14/2023] [Indexed: 04/08/2023]
Abstract
MYC's key role in oncogenesis and tumor progression has long been established for most human cancers. In melanoma, its deregulated activity by amplification of 8q24 chromosome or by upstream signaling coming from activating mutations in the RAS/RAF/MAPK pathway-the most predominantly mutated pathway in this disease-turns MYC into not only a driver but also a facilitator of melanoma progression, with documented effects leading to an aggressive clinical course and resistance to targeted therapy. Here, by making use of Omomyc, the most characterized MYC inhibitor to date that has just successfully completed a phase I clinical trial, we show for the first time that MYC inhibition in melanoma induces remarkable transcriptional modulation, resulting in severely compromised tumor growth and a clear abrogation of metastatic capacity independently of the driver mutation. By reducing MYC's transcriptional footprint in melanoma, Omomyc elicits gene expression profiles remarkably similar to those of patients with good prognosis, underlining the therapeutic potential that such an approach could eventually have in the clinic in this dismal disease.
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Affiliation(s)
- Mariano F Zacarías-Fluck
- Models of Cancer Therapies Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain;
| | - Daniel Massó-Vallés
- Models of Cancer Therapies Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Peptomyc SL, Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Fabio Giuntini
- Models of Cancer Therapies Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Íñigo González-Larreategui
- Models of Cancer Therapies Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Department of Cellular Biology, Phisiology and Immunology, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Jastrinjan Kaur
- Models of Cancer Therapies Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Sílvia Casacuberta-Serra
- Models of Cancer Therapies Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Peptomyc SL, Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Toni Jauset
- Models of Cancer Therapies Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Peptomyc SL, Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Sandra Martínez-Martín
- Models of Cancer Therapies Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Peptomyc SL, Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Génesis Martín-Fernández
- Models of Cancer Therapies Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Peptomyc SL, Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Erika Serrano Del Pozo
- Models of Cancer Therapies Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Laia Foradada
- Peptomyc SL, Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Judit Grueso
- Models of Cancer Therapies Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Peptomyc SL, Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Lara Nonell
- Bioinformatics Unit, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Marie-Eve Beaulieu
- Models of Cancer Therapies Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Peptomyc SL, Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Jonathan R Whitfield
- Models of Cancer Therapies Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Laura Soucek
- Models of Cancer Therapies Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain;
- Peptomyc SL, Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08035 Barcelona, Spain
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5
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Viasus D, Simonetti AF, Nonell L, Vidal O, Meije Y, Ortega L, Arnal M, Bódalo-Torruella M, Sierra M, Rombauts A, Abelenda-Alonso G, Blanchart G, Gudiol C, Carratalà J. Whole-Blood Gene Expression Profiles Associated with Mortality in Community-Acquired Pneumonia. Biomedicines 2023; 11:biomedicines11020429. [PMID: 36830965 PMCID: PMC9953679 DOI: 10.3390/biomedicines11020429] [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: 12/05/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023] Open
Abstract
(1) Background: Information regarding gene expression profiles and the prognosis of community-acquired pneumonia (CAP) is scarce. We aimed to examine the differences in the gene expression profiles in peripheral blood at hospital admission between patients with CAP who died during hospitalization and those who survived. (2) Methods: This is a multicenter study of nonimmunosuppressed adult patients who required hospitalization for CAP. Whole blood samples were obtained within 24 h of admission for genome-expression-profile analysis. Gene expression profiling identified both differentially expressed genes and enriched gene sets. (3) Results: A total of 198 samples from adult patients who required hospitalization for CAP were processed, of which 13 were from patients who died. Comparison of gene expression between patients who died and those who survived yielded 49 differentially expressed genes, 36 of which were upregulated and 13 downregulated. Gene set enrichment analysis (GSEA) identified four positively enriched gene sets in survivors, mainly associated with the interferon-alpha response, apoptosis, and sex hormone pathways. Similarly, GSEA identified seven positively enriched gene sets, associated with the oxidative stress, endoplasmic reticulum stress, oxidative phosphorylation, and angiogenesis pathways, in the patients who died. Protein-protein-interaction-network analysis identified FOS, CDC42, SLC26A10, EIF4G2, CCND3, ASXL1, UBE2S, and AURKA as the main gene hubs. (4) Conclusions: We found differences in gene expression profiles at hospital admission between CAP patients who died and those who survived. Our findings may help to identify novel candidate pathways and targets for potential intervention and biomarkers for risk stratification.
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Affiliation(s)
- Diego Viasus
- Department of Medicine, Division of Health Sciences, Universidad del Norte and Hospital Universidad del Norte, Barranquilla 081001, Colombia
- Correspondence:
| | - Antonella F. Simonetti
- Department of Internal Medicine, Consorci Sanitari Alt Penedès-Garraf, 08720 Sant Pere de Ribes, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Institulo de Salud Carlos III, 28029 Madrid, Spain
| | - Lara Nonell
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Oscar Vidal
- Department of Medicine, Division of Health Sciences, Universidad del Norte and Hospital Universidad del Norte, Barranquilla 081001, Colombia
| | - Yolanda Meije
- Unit of Infectious Disease, Department of Internal Medicine, Hospital de Barcelona—Societat Cooperativa d’Instal·lacions Assistencials Sanitàries (SCIAS), 08029 Barcelona, Spain
| | - Lucía Ortega
- Unit of Infectious Disease, Department of Internal Medicine, Hospital de Barcelona—Societat Cooperativa d’Instal·lacions Assistencials Sanitàries (SCIAS), 08029 Barcelona, Spain
| | - Magdalena Arnal
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | | | - Montserrat Sierra
- Microbiology Unit, Department of Clinical Laboratory, Hospital de Barcelona—Societat Cooperativa d’Instal·lacions Assistencials Sanitàries (SCIAS), 08029 Barcelona, Spain
| | - Alexander Rombauts
- Department of Infectious Diseases, Bellvitge University Hospital—Bellvitge Biomedical Research Institute (IDIBELL), 08907 Barcelona, Spain
| | - Gabriela Abelenda-Alonso
- Department of Infectious Diseases, Bellvitge University Hospital—Bellvitge Biomedical Research Institute (IDIBELL), 08907 Barcelona, Spain
| | - Gemma Blanchart
- Cardiovascular Risk and Nutrition Research Group, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Carlota Gudiol
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Institulo de Salud Carlos III, 28029 Madrid, Spain
- Department of Infectious Diseases, Bellvitge University Hospital—Bellvitge Biomedical Research Institute (IDIBELL), 08907 Barcelona, Spain
- Department of Clinical Sciences, University of Barcelona, 08907 Barcelona, Spain
| | - Jordi Carratalà
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Institulo de Salud Carlos III, 28029 Madrid, Spain
- Department of Infectious Diseases, Bellvitge University Hospital—Bellvitge Biomedical Research Institute (IDIBELL), 08907 Barcelona, Spain
- Department of Clinical Sciences, University of Barcelona, 08907 Barcelona, Spain
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6
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Sathyanarayanan A, Mueller TT, Ali Moni M, Schueler K, Baune BT, Lio P, Mehta D, Baune BT, Dierssen M, Ebert B, Fabbri C, Fusar-Poli P, Gennarelli M, Harmer C, Howes OD, Janzing JGE, Lio P, Maron E, Mehta D, Minelli A, Nonell L, Pisanu C, Potier MC, Rybakowski F, Serretti A, Squassina A, Stacey D, van Westrhenen R, Xicota L. Multi-omics data integration methods and their applications in psychiatric disorders. Eur Neuropsychopharmacol 2023; 69:26-46. [PMID: 36706689 DOI: 10.1016/j.euroneuro.2023.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/22/2022] [Accepted: 01/02/2023] [Indexed: 01/27/2023]
Abstract
To study mental illness and health, in the past researchers have often broken down their complexity into individual subsystems (e.g., genomics, transcriptomics, proteomics, clinical data) and explored the components independently. Technological advancements and decreasing costs of high throughput sequencing has led to an unprecedented increase in data generation. Furthermore, over the years it has become increasingly clear that these subsystems do not act in isolation but instead interact with each other to drive mental illness and health. Consequently, individual subsystems are now analysed jointly to promote a holistic understanding of the underlying biological complexity of health and disease. Complementing the increasing data availability, current research is geared towards developing novel methods that can efficiently combine the information rich multi-omics data to discover biologically meaningful biomarkers for diagnosis, treatment, and prognosis. However, clinical translation of the research is still challenging. In this review, we summarise conventional and state-of-the-art statistical and machine learning approaches for discovery of biomarker, diagnosis, as well as outcome and treatment response prediction through integrating multi-omics and clinical data. In addition, we describe the role of biological model systems and in silico multi-omics model designs in clinical translation of psychiatric research from bench to bedside. Finally, we discuss the current challenges and explore the application of multi-omics integration in future psychiatric research. The review provides a structured overview and latest updates in the field of multi-omics in psychiatry.
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Affiliation(s)
- Anita Sathyanarayanan
- Queensland University of Technology, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Kelvin Grove, Queensland 4059, Australia
| | - Tamara T Mueller
- Institute for Artificial Intelligence and Informatics in Medicine, TU Munich, 80333 Munich, Germany
| | - Mohammad Ali Moni
- Artificial Intelligence and Digital Health Data Science, School of Health and Rehabilitation Sciences, Faculty of Health and Behavioural Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Katja Schueler
- Clinic for Psychosomatics, Hospital zum Heiligen Geist, Frankfurt am Main, Germany; Frankfurt Psychoanalytic Institute, Frankfurt am Main, Germany
| | - Bernhard T Baune
- Department of Psychiatry and Psychotherapy, University of Münster, Germany; Department of Psychiatry, Melbourne Medical School, University of Melbourne, Australia; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Australia
| | - Pietro Lio
- Department of Computer Science and Technology, University of Cambridge, Cambridge, United Kingdom
| | - Divya Mehta
- Queensland University of Technology, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Kelvin Grove, Queensland 4059, Australia.
| | | | - Bernhard T Baune
- Department of Psychiatry and Psychotherapy, University of Münster, Germany; Department of Psychiatry, Melbourne Medical School, University of Melbourne, Australia; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Australia
| | - Mara Dierssen
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Bjarke Ebert
- Medical Strategy & Communication, H. Lundbeck A/S, Valby, Denmark
| | - Chiara Fabbri
- Department of Biomedical and NeuroMotor Sciences, University of Bologna, Bologna, Italy; Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Paolo Fusar-Poli
- Early Psychosis: Intervention and Clinical-detection (EPIC) Lab, Department of Psychosis Studies, King's College London, United Kingdom; Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Massimo Gennarelli
- Department of Molecular and Translational Medicine, University of Brescia; Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | | | - Oliver D Howes
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom; Psychiatric Imaging, Medical Research Council Clinical Sciences Centre, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | | | - Pietro Lio
- Department of Computer Science and Technology, University of Cambridge, Cambridge, United Kingdom
| | - Eduard Maron
- Department of Psychiatry, University of Tartu, Tartu, Estonia; Centre for Neuropsychopharmacology, Division of Brain Sciences, Imperial College London, London, United Kingdom; Documental Ltd, Tallin, Estonia; West Tallinn Central Hospital, Tallinn, Estonia
| | - Divya Mehta
- Queensland University of Technology, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Kelvin Grove, Queensland 4059, Australia
| | - Alessandra Minelli
- Department of Molecular and Translational Medicine, University of Brescia; Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Lara Nonell
- MARGenomics, IMIM (Hospital del Mar Research Institute), Barcelona, Spain
| | - Claudia Pisanu
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
| | | | - Filip Rybakowski
- Department of Psychiatry, Poznan University of Medical Sciences, Poznan, Poland
| | - Alessandro Serretti
- Department of Biomedical and NeuroMotor Sciences, University of Bologna, Bologna, Italy
| | - Alessio Squassina
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
| | - David Stacey
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Roos van Westrhenen
- Parnassia Psychiatric Institute, Amsterdam, the Netherlands; Department of Psychiatry and Neuropsychology, Faculty of Health and Sciences, Maastricht University, Maastricht, the Netherlands; Institute of Psychiatry, Psychology & Neuroscience (IoPPN) King's College London, United Kingdom
| | - Laura Xicota
- Paris Brain Institute ICM, Salpetriere Hospital, Paris, France
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7
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Andrades E, Clarós M, Torres JV, Nonell L, González M, Curto-Barredo L, Rozas-Muñoz E, Gimeno R, Barranco C, Pujol RM, Izquierdo I, Giménez-Arnau AM. New transcriptome and clinical findings of platelet-activating factor in chronic spontaneous urticaria: Pathogenic and treatment relevance. Biofactors 2022; 48:1284-1294. [PMID: 35927787 DOI: 10.1002/biof.1880] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/15/2022] [Indexed: 12/24/2022]
Abstract
The objective of the study was to assess the pathogenic and treatment relevance of Platelet Activating factor (PAF) in chronic spontaneous urticaria (CSU). The expression and cellular location of PAF receptor (PAFR) and serum levels of PAF and PAF acetylhydrolase (PAF-AH) in patients with moderate/severe CSU (n = 45) and healthy controls (HCs, n = 17) were studied. Skin samples from the active wheal (LS-CSU, 13 samples for qPCR and 33 for immunohistochemistry) and non-lesional skin (NLS-CSU, 13 samples) of CSU patients and HCs (13 samples and 5 for immunohistochemistry) were analyzed. Serum PAF and PAF-AH levels were measured by ELISA and compared between HC (10 samples) and CSU patients (25 samples) and, among them, between those refractory and non-refractory to second-generation H1 -antihistamines (sgAH). PAFR mRNA expression was significantly higher in LS-CSU versus HCs (p = 0.014). PAFR positive staining in immunohistochemistry was mainly found in the epidermal basal layer in HCs, whereas it was broadly present along the epidermis in LS-CSU samples. Endothelial cells showed PAFR expression exclusively in LS-CSU and NLS-CSU samples. PAFR expression was observed in the nerves of HC, LS-CSU, and NLS-CSU samples. Double PAFR/CD43 expression showed that T-lymphocytes were the main cell type from the wheal inflammatory infiltrate expressing PAFR. A significantly lower PAF-AH/PAF ratio was observed in sgAH non-responders versus responders (6.1 vs. 12.6; p = 0.049). Our study confirms that PAF is a mediator of wheal pathogenesis in CSU. The significantly lower PAF-AH/PAF ratio in sgAH non-responders vs responders suggests that PAF could be a potential biomarker of sgAH refractoriness.
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Affiliation(s)
- Evelyn Andrades
- Department of Dermatology, Hospital del Mar, Universitat Autònoma de Barcelona and Universitat Pompeu Fabra, Barcelona, Spain
- Group of Inflammatory and Neoplastic Dermatological Diseases, Institut Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Miquel Clarós
- Microarray Analysis Service, Institut Mar d'Investigacions Mèdiques, Barcelona, Spain
| | | | - Lara Nonell
- Bioinformatics Unit, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Mónica González
- Department of Pathology, Hospital del Mar, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Laia Curto-Barredo
- Department of Dermatology, Hospital del Mar, Universitat Autònoma de Barcelona and Universitat Pompeu Fabra, Barcelona, Spain
- Group of Inflammatory and Neoplastic Dermatological Diseases, Institut Mar d'Investigacions Mèdiques, Barcelona, Spain
| | | | - Ramon Gimeno
- Department of Immunology, Hospital del Mar-Institut Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Carlos Barranco
- Department of Pathology, Hospital del Mar, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ramon M Pujol
- Department of Dermatology, Hospital del Mar, Universitat Autònoma de Barcelona and Universitat Pompeu Fabra, Barcelona, Spain
- Group of Inflammatory and Neoplastic Dermatological Diseases, Institut Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Iñaki Izquierdo
- Departament of Clinical Development & Medical Advice, Biohorm SL Palau-Solità i Plegamans, Barcelona, Spain
| | - Ana M Giménez-Arnau
- Department of Dermatology, Hospital del Mar, Universitat Autònoma de Barcelona and Universitat Pompeu Fabra, Barcelona, Spain
- Group of Inflammatory and Neoplastic Dermatological Diseases, Institut Mar d'Investigacions Mèdiques, Barcelona, Spain
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Martínez Martín S, López-Estévez S, Foradada L, Kaur J, Serrano E, González-Larreategui Í, Giuntini F, Casacuberta-Serra S, Thabussot H, Castillo Cano V, Nonell L, Soucek L, Beaulieu M. Omomyc downregulates MYC transcriptional signature in preclinical models of solid tumours and shows long half-life in tumour tissue. Eur J Cancer 2022. [DOI: 10.1016/s0959-8049(22)00918-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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9
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Martínez-Sabadell A, Morancho B, Rius Ruiz I, Román Alonso M, Ovejero Romero P, Escorihuela M, Chicote I, Palmer HG, Nonell L, Alemany-Chavarria M, Klein C, Bacac M, Arribas J, Arenas EJ. The target antigen determines the mechanism of acquired resistance to T cell-based therapies. Cell Rep 2022; 41:111430. [DOI: 10.1016/j.celrep.2022.111430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 06/20/2022] [Accepted: 09/08/2022] [Indexed: 11/03/2022] Open
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10
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Font A, Ruiz de Porras V, Valderrama BP, Ramirez JL, Nonell L, Virizuela JA, Anido U, González-del-Alba A, Lainez N, Llorente MDM, Jiménez N, Mellado B, García-Donas J, Bellmunt J. Epithelial-to-Mesenchymal Transition Mediates Resistance to Maintenance Therapy with Vinflunine in Advanced Urothelial Cell Carcinoma. Cancers (Basel) 2021; 13:cancers13246235. [PMID: 34944855 PMCID: PMC8699401 DOI: 10.3390/cancers13246235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/03/2021] [Accepted: 12/10/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Platinum-based chemotherapy is the first-line treatment for advanced urothelial cell carcinoma (aUCC). After first-line treatment, we previously showed that maintenance therapy with vinflunine improves progression-free survival. However, some patients are resistant to vinflunine and the specific mechanisms of resistance in aUCC are unclear. We analyzed the genomic landscape and the biological processes potentially related to vinflunine activity and found that epithelial-to-mesenchymal transition (EMT) plays a pivotal role as a resistance mechanism. In experiments with cell lines, curcumin reversed EMT and sensitized cells to vinflunine. We suggest that EMT mediates resistance to vinflunine and that the reversion of this process could enhance the effect of vinflunine in aUCC patients. Abstract In the phase II MAJA trial, maintenance therapy with vinflunine resulted in longer progression-free survival compared to best supportive care in advanced urothelial cell carcinoma (aUCC) patients who did not progress after first-line platinum-based chemotherapy. However, despite an initial benefit observed in some patients, unequivocal resistance appears which underlying mechanisms are presently unknown. We have performed gene expression and functional enrichment analyses to shed light on the discovery of these underlying resistance mechanisms. Differential gene expression profile of eight patients with poor outcome and nine with good outcome to vinflunine administered in the MAJA trial were analyzed. RNA was isolated from tumor tissue and gene expression was assessed by microarray. Differential expression was determined with linear models for microarray data. Gene Set Enrichment Analysis (GSEA) was used for the functional classification of the genes. In vitro functional studies were performed using UCC cell lines. Hierarchical clustering showed a differential gene expression pattern between patients with good and poor outcome to vinflunine treatment. GSEA identified epithelial-to-mesenchymal transition (EMT) as the top negatively enriched hallmark in patients with good outcome. In vitro analyses showed that the polyphenol curcumin downregulated EMT markers and sensitized UCC cells to vinflunine. We conclude that EMT mediates resistance to vinflunine and suggest that the reversion of this process could enhance the effect of vinflunine in aUCC patients.
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Affiliation(s)
- Albert Font
- Department of Medical Oncology, Catalan Institute of Oncology, University Hospital Germans Trias i Pujol, Ctra. Can Ruti-Camí de les Escoles s/n, 08916 Badalona, Spain;
- Catalan Institute of Oncology, Badalona Applied Research Group in Oncology (B·ARGO), Ctra. Can Ruti-Camí de les Escoles s/n, 08916 Badalona, Spain;
| | - Vicenç Ruiz de Porras
- Catalan Institute of Oncology, Badalona Applied Research Group in Oncology (B·ARGO), Ctra. Can Ruti-Camí de les Escoles s/n, 08916 Badalona, Spain;
- Germans Trias i Pujol Research Institute (IGTP), Ctra. Can Ruti-Camí de les Escoles s/n, 08916 Badalona, Spain
| | - Begoña P. Valderrama
- Department of Medical Oncology, Hospital Universitario Virgen del Rocío, 41013 Seville, Spain;
| | - Jose Luis Ramirez
- Department of Haematology, Catalan Institute of Oncology, University Hospital Germans Trias i Pujol, Ctra. Can Ruti-Camí de les Escoles s/n, 08916 Badalona, Spain;
| | - Lara Nonell
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain;
| | - José Antonio Virizuela
- Department of Medical Oncology, Hospital Universitario Virgen de Macarena, 41009 Seville, Spain;
| | - Urbano Anido
- Department of Medical Oncology, Complejo Hospitalario Universitario de Santiago, 15706 Santiago de Compostela, Spain;
| | - Aránzazu González-del-Alba
- Department of Medical Oncology, Hospital Universitario Puerta de Hierro-Majadahonda, 28222 Madrid, Spain;
| | - Nuria Lainez
- Department of Medical Oncology, Complejo Hospitalario de Navarra, 31008 Pamplona, Spain;
| | - Maria del Mar Llorente
- Department of Medical Oncology, Hospital General Universitario de Elda, 03600 Alicante, Spain;
| | - Natalia Jiménez
- Translational Genomics and Targeted Therapeutics in Solid Tumors Laboratory, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain;
| | - Begoña Mellado
- Department of Medical Oncology, Hospital Clinic de Barcelona, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain;
| | - Jesus García-Donas
- Division of Medical Oncology, HM Hospitales-Centro Integral Oncológico Hospital de Madrid Clara Campal, 28050 Madrid, Spain
- Correspondence: (J.G.D.); (J.B.)
| | - Joaquim Bellmunt
- Division of Hematology and Oncology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
- Correspondence: (J.G.D.); (J.B.)
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11
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Hernández-Llodrà S, Segalés L, Juanpere N, Marta Lorenzo T, Salido M, Nonell L, David López T, Rodríguez-Vida A, Bellmunt J, Fumadó L, Cecchini L, Lloreta-Trull J. SPOP and CHD1 alterations in prostate cancer: Relationship with PTEN loss, tumor grade, perineural infiltration, and PSA recurrence. Prostate 2021; 81:1267-1277. [PMID: 34533858 DOI: 10.1002/pros.24218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 05/06/2021] [Accepted: 08/16/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND In the non-ETS fusion of prostate cancer (PCa) pathway, SPOP mutations emerge as a distinct oncogenic driver subclass. Both SPOP downregulation and mutation can lead to SPOP target stabilization promoting dysregulation of key regulatory pathways. CHD1 gene is commonly deleted in PCa. CHD1 loss significantly co-occurs with SPOP mutations, resulting in a PCa subclass with increased AR transcriptional activity and with a specific epigenetic pattern. METHODS In this study, SPOP alterations at mutational and protein levels and CHD1 copy number alterations have been analyzed and correlated with ERG and PTEN protein expression and with the clinical pathological features of the patients. RESULTS SPOP protein loss has been detected in 42.9% of the cases, and it has been strongly associated with PTEN protein loss (p < .001). CHD1 gene loss has been detected in 24.5% and SPOP mutations in 5.9% of the cases. Loss of CHD1 has been strongly associated with SPOP mutations (p = .003) and has shown a trend to be associated with ERG wt cancers (p = .08). The loss of SPOP protein (p = .01) and the combination of PTEN and SPOP protein loss (p = .002) were both statistically more common in grade group 5 cancers, with a prevalence of 60% and 37.5%, respectively. Furthermore, SPOP loss/PTEN loss and SPOP wt/PTEN loss phenotypes were strongly associated with extraprostatic perineural infiltration (p = .007). Strong CHD1 loss was associated with a shorter time to PSA recurrence in the univariate (p = .04), and showed a trend to be associated with the PSA recurrence risk in the multivariate analysis (p = .058). CONCLUSIONS The results of the present study suggest that the loss of SPOP protein expression, either alone or in combination with loss of PTEN and, on the other hand, a marked loss of the CHD1 gene are very promising prognostic biomarkers in PCa.
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Affiliation(s)
| | - Laura Segalés
- Departament of Health and Experimental Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Nuria Juanpere
- Departament of Health and Experimental Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Department of Pathology, Hospital del Mar-Parc de Salut Mar-IMIM, Barcelona, Spain
| | | | - Marta Salido
- Department of Pathology, Hospital del Mar-Parc de Salut Mar-IMIM, Barcelona, Spain
| | - Lara Nonell
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Tech David López
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Alejo Rodríguez-Vida
- Department of Medical Oncology, Hospital del Mar-Parc de Salut Mar-IMIM, Barcelona, Spain
| | - Joaquim Bellmunt
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Department of Medical Oncology, Harvard Medical School, Hospital Beth Israel, Boston, Massachusetts, USA
| | - Lluís Fumadó
- Department of Urology, Hospital del Mar-Parc de Salut Mar-IMIM, Barcelona, Spain
| | - Lluís Cecchini
- Department of Urology, Hospital del Mar-Parc de Salut Mar-IMIM, Barcelona, Spain
| | - Josep Lloreta-Trull
- Departament of Health and Experimental Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Department of Pathology, Hospital del Mar-Parc de Salut Mar-IMIM, Barcelona, Spain
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12
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Gil-Gómez G, Fassan M, Nonell L, Garrido M, Climent M, Anglada R, Iglesias M, Guzzardo V, Borga C, Grande L, de Bolós C, Pera M. miR-24-3p regulates CDX2 during intestinalization of cardiac-type epithelium in a human model of Barrett's esophagus. Dis Esophagus 2021; 34:6131383. [PMID: 33558874 DOI: 10.1093/dote/doab005] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/15/2020] [Accepted: 01/07/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Cardiac-type epithelium has been proposed as the precursor of intestinal metaplasia in the development of Barrett's esophagus. Dysregulation of microRNAs (miRNAs) and their effects on CDX2 expression may contribute to intestinalization of cardiac-type epithelium. The aim of this study was to examine the possible effect of specific miRNAs on the regulation of CDX2 in a human model of Barrett's esophagus. METHODS Microdissection of cardiac-type glands was performed in biopsy samples from patients who underwent esophagectomy and developed cardiac-type epithelium in the remnant esophagus. OpenArray™ analysis was used to compare the miRNAs profiling of cardiac-type glands with negative or fully positive CDX2 expression. CDX2 was validated as a miR-24 messenger RNA target by the study of CDX2 expression upon transfection of miRNA mimics and inhibitors in esophageal adenocarcinoma cell lines. The CDX2/miR-24 regulation was finally validated by in situ miRNA/CDX2/MUC2 co-expression analysis in cardiac-type mucosa samples of Barrett's esophagus. RESULTS CDX2 positive glands were characterized by a unique miRNA profile with a significant downregulation of miR-24-3p, miR-30a-5p, miR-133a-3p, miR-520e-3p, miR-548a-1, miR-597-5p, miR-625-3p, miR-638, miR-1255b-1, and miR-1260a, as well as upregulation of miR-590-5p. miRNA-24-3p was identified as potential regulator of CDX2 gene expression in three databases and confirmed in esophageal adenocarcinoma cell lines. Furthermore, miR-24-3p expression showed a negative correlation with the expression of CDX2 in cardiac-type mucosa samples with different stages of mucosal intestinalization. CONCLUSION These results showed that miRNA-24-3p regulates CDX2 expression, and the downregulation of miRNA-24-3p was associated with the acquisition of the intestinal phenotype in esophageal cardiac-type epithelium.
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Affiliation(s)
- Gabriel Gil-Gómez
- Gastroesophageal Carcinogenesis Research Group, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology and Cytopathology Unit, University of Padua, Padua, Italy
| | - Lara Nonell
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Marta Garrido
- Gastroesophageal Carcinogenesis Research Group, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Marta Climent
- Gastroesophageal Carcinogenesis Research Group, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain.,Section of Gastrointestinal Surgery, Hospital Universitario del Mar, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Roger Anglada
- Genomics Core Facility, Universitat Pompeu Fabra, Barcelona, Spain
| | - Mar Iglesias
- Gastroesophageal Carcinogenesis Research Group, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain.,Department of Pathology, Hospital Universitario del Mar, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Vicenza Guzzardo
- Department of Medicine (DIMED), Surgical Pathology and Cytopathology Unit, University of Padua, Padua, Italy
| | - Chiara Borga
- Department of Medicine (DIMED), Surgical Pathology and Cytopathology Unit, University of Padua, Padua, Italy
| | - Luis Grande
- Section of Gastrointestinal Surgery, Hospital Universitario del Mar, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Carme de Bolós
- Gastroesophageal Carcinogenesis Research Group, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Manuel Pera
- Gastroesophageal Carcinogenesis Research Group, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain.,Section of Gastrointestinal Surgery, Hospital Universitario del Mar, Universitat Autònoma de Barcelona, Barcelona, Spain
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13
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Palou-Márquez G, Subirana I, Nonell L, Fernández-Sanlés A, Elosua R. DNA methylation and gene expression integration in cardiovascular disease. Clin Epigenetics 2021; 13:75. [PMID: 33836805 PMCID: PMC8034168 DOI: 10.1186/s13148-021-01064-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/29/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The integration of different layers of omics information is an opportunity to tackle the complexity of cardiovascular diseases (CVD) and to identify new predictive biomarkers and potential therapeutic targets. Our aim was to integrate DNA methylation and gene expression data in an effort to identify biomarkers related to cardiovascular disease risk in a community-based population. We accessed data from the Framingham Offspring Study, a cohort study with data on DNA methylation (Infinium HumanMethylation450 BeadChip; Illumina) and gene expression (Human Exon 1.0 ST Array; Affymetrix). Using the MOFA2 R package, we integrated these data to identify biomarkers related to the risk of presenting a cardiovascular event. RESULTS Four independent latent factors (9, 19, 21-only in women-and 27), driven by DNA methylation, were associated with cardiovascular disease independently of classical risk factors and cell-type counts. In a sensitivity analysis, we also identified factor 21 as associated with CVD in women. Factors 9, 21 and 27 were also associated with coronary heart disease risk. Moreover, in a replication effort in an independent study three of the genes included in factor 27 were also present in a factor identified to be associated with myocardial infarction (CDC42BPB, MAN2A2 and RPTOR). Factor 9 was related to age and cell-type proportions; factor 19 was related to age and B cells count; factor 21 pointed to human immunodeficiency virus infection-related pathways and inflammation; and factor 27 was related to lifestyle factors such as alcohol consumption, smoking and body mass index. Inclusion of factor 21 (only in women) improved the discriminative and reclassification capacity of the Framingham classical risk function and factor 27 improved its discrimination. CONCLUSIONS Unsupervised multi-omics data integration methods have the potential to provide insights into the pathogenesis of cardiovascular diseases. We identified four independent factors (one only in women) pointing to inflammation, endothelium homeostasis, visceral fat, cardiac remodeling and lifestyles as key players in the determination of cardiovascular risk. Moreover, two of these factors improved the predictive capacity of a classical risk function.
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Affiliation(s)
- Guillermo Palou-Márquez
- Cardiovascular Epidemiology and Genetics Research Group, Hospital del Mar Medical Research Institute (IMIM), Dr Aiguader 88, 08003, Barcelona, Spain
- Pompeu Fabra University (UPF), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Isaac Subirana
- Cardiovascular Epidemiology and Genetics Research Group, Hospital del Mar Medical Research Institute (IMIM), Dr Aiguader 88, 08003, Barcelona, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Barcelona, Spain
| | - Lara Nonell
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Alba Fernández-Sanlés
- Cardiovascular Epidemiology and Genetics Research Group, Hospital del Mar Medical Research Institute (IMIM), Dr Aiguader 88, 08003, Barcelona, Spain
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
| | - Roberto Elosua
- Cardiovascular Epidemiology and Genetics Research Group, Hospital del Mar Medical Research Institute (IMIM), Dr Aiguader 88, 08003, Barcelona, Spain.
- CIBER Cardiovascular Diseases (CIBERCV), Barcelona, Spain.
- Medicine Department, Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain.
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14
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Martín-Sánchez A, Piñero J, Nonell L, Arnal M, Ribe EM, Nevado-Holgado A, Lovestone S, Sanz F, Furlong LI, Valverde O. Comorbidity between Alzheimer's disease and major depression: a behavioural and transcriptomic characterization study in mice. Alzheimers Res Ther 2021; 13:73. [PMID: 33795014 PMCID: PMC8017643 DOI: 10.1186/s13195-021-00810-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/17/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Major depression (MD) is the most prevalent psychiatric disease in the population and is considered a prodromal stage of the Alzheimer's disease (AD). Despite both diseases having a robust genetic component, the common transcriptomic signature remains unknown. METHODS We investigated the cognitive and emotional behavioural responses in 3- and 6-month-old APP/PSEN1-Tg mice, before β-amyloid plaques were detected. We studied the genetic and pathway deregulation in the prefrontal cortex, striatum, hippocampus and amygdala of mice at both ages, using transcriptomic and functional data analysis. RESULTS We found that depressive-like and anxiety-like behaviours, as well as memory impairments, are already present at 3-month-old APP/PSEN1-Tg mutant mice together with the deregulation of several genes, such as Ciart, Grin3b, Nr1d1 and Mc4r, and other genes including components of the circadian rhythms, electron transport chain and neurotransmission in all brain areas. Extending these results to human data performing GSEA analysis using DisGeNET database, it provides translational support for common deregulated gene sets related to MD and AD. CONCLUSIONS The present study sheds light on the shared genetic bases between MD and AD, based on a comprehensive characterization from the behavioural to transcriptomic level. These findings suggest that late MD could be an early manifestation of AD.
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Affiliation(s)
- Ana Martín-Sánchez
- Neurobiology of Behaviour Research Group (GReNeC-NeuroBio), Department of Experimental and Health Science, Universitat Pompeu Fabra, Carrer Dr Aiguader 88, 08003, Barcelona, Spain
- Neuroscience Research Program, IMIM-Hospital del Mar Research Institute, Barcelona, Spain
| | - Janet Piñero
- Research Programme on Biomedical Informatics (GRIB), IMIM-Hospital del Mar Medical Research Institute, Universitat Pompeu Fabra, Barcelona, Spain
| | - Lara Nonell
- Research Programme on Biomedical Informatics (GRIB), IMIM-Hospital del Mar Medical Research Institute, Universitat Pompeu Fabra, Barcelona, Spain
- MARGenomics core facility, IMIM-Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Magdalena Arnal
- Research Programme on Biomedical Informatics (GRIB), IMIM-Hospital del Mar Medical Research Institute, Universitat Pompeu Fabra, Barcelona, Spain
| | - Elena M Ribe
- Department of Psychiatry, University of Oxford, Oxford, OX3 7JX, UK
| | - Alejo Nevado-Holgado
- Department of Psychiatry, University of Oxford, Oxford, OX3 7JX, UK
- Oxford Health NHS Foundation Trust, Oxford, OX3 7JX, UK
| | - Simon Lovestone
- Department of Psychiatry, University of Oxford, Oxford, OX3 7JX, UK
- Johnson and Johnson Medical Ltd., Janssen-Cilag, High Wycombe, UK
| | - Ferran Sanz
- Research Programme on Biomedical Informatics (GRIB), IMIM-Hospital del Mar Medical Research Institute, Universitat Pompeu Fabra, Barcelona, Spain
| | - Laura I Furlong
- Research Programme on Biomedical Informatics (GRIB), IMIM-Hospital del Mar Medical Research Institute, Universitat Pompeu Fabra, Barcelona, Spain
| | - Olga Valverde
- Neurobiology of Behaviour Research Group (GReNeC-NeuroBio), Department of Experimental and Health Science, Universitat Pompeu Fabra, Carrer Dr Aiguader 88, 08003, Barcelona, Spain.
- Neuroscience Research Program, IMIM-Hospital del Mar Research Institute, Barcelona, Spain.
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15
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Puiggros A, Blanco G, Muntasell A, Rodríguez-Rivera M, Nonell L, Altadill M, Puigdecanet E, Arnal M, Calvo X, Gimeno E, Abella E, Abrisqueta P, Bosch F, Yélamos J, Ferrer A, López-Botet M, Espinet B. Reduced expansion of CD94/NKG2C + NK cells in chronic lymphocytic leukemia and CLL-like monoclonal B-cell lymphocytosis is not related to increased human cytomegalovirus seronegativity or NKG2C deletions. Int J Lab Hematol 2021; 43:1032-1040. [PMID: 33615729 DOI: 10.1111/ijlh.13494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/29/2021] [Accepted: 02/06/2021] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Dysregulated NK cell-mediated immune responses contribute to tumor evasion in chronic lymphocytic leukemia (CLL), although the NK cell compartment in CLL-like monoclonal B-cell lymphocytosis (MBL) is poorly understood. In healthy individuals, human cytomegalovirus (HCMV) induces the expansion of NK cells expressing high levels of CD94/NKG2C NK cell receptor (NKR) specific for HLA-E. METHODS We analyzed the expression of NKG2A, NKG2C, ILT2, KIR, CD161, and CD57 in 24 MBL and 37 CLL. NKG2C was genotyped in these patients and in 81 additional MBL/CLL, while NKG2C gene expression was assessed in 26 cases. In 8 CLL patients with increased lymphocytosis (≥20 × 109 /L), tumor HLA-E and HLA-G expression was evaluated. RESULTS NKR distribution did not significantly differ between MBL and CLL patients, although they exhibited reduced NKG2C+ NK cells compared with a non-CLL group (4.6% vs 12.2%, P = .012). HCMV+ patients showed increased percentages of NKG2C+ NK cells compared with HCMV- (7.3% vs 2.9%, P = .176). Frequencies of NKG2C deletions in MBL/CLL were similar to those of the general population. Low/undetectable NKG2C expression was found among NKG2C+/- (45%) and NKG2C+/+ (12%) patients. CLL cases with increased lymphocytosis displayed especially reduced NKG2C expression (1.8% vs 8.1%, P = .029) and tumor cells with high HLA-E (>98%) and variable HLA-G expression (12.4%, range: 0.5-56.4). CLL patients with low NKG2C expression (<7%) showed shorter time to first treatment (P = .037). CONCLUSION Reduced percentages of CD94/NKG2C+ NK cells were observed in CLL and MBL patients independently of HCMV serostatus and NKG2C zygosity, particularly in CLL patients with increased lymphocytosis, which could potentially be related to the exposure to tumor cells.
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Affiliation(s)
- Anna Puiggros
- Molecular Cytogenetics Laboratory, Hematological Cytology Laboratory, Pathology Department, Hospital del Mar, Barcelona, Spain.,Translational Research on Hematological Neoplasms Group, Cancer Research Program, IMIM-Hospital del Mar, Barcelona, Spain
| | - Gonzalo Blanco
- Molecular Cytogenetics Laboratory, Hematological Cytology Laboratory, Pathology Department, Hospital del Mar, Barcelona, Spain.,Translational Research on Hematological Neoplasms Group, Cancer Research Program, IMIM-Hospital del Mar, Barcelona, Spain
| | - Aura Muntasell
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - María Rodríguez-Rivera
- Molecular Cytogenetics Laboratory, Hematological Cytology Laboratory, Pathology Department, Hospital del Mar, Barcelona, Spain.,Translational Research on Hematological Neoplasms Group, Cancer Research Program, IMIM-Hospital del Mar, Barcelona, Spain
| | | | | | - Eulàlia Puigdecanet
- MARGenomics, IMIM, Barcelona, Spain.,Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Barcelona, Spain
| | | | - Xavier Calvo
- Molecular Cytogenetics Laboratory, Hematological Cytology Laboratory, Pathology Department, Hospital del Mar, Barcelona, Spain.,Translational Research on Hematological Neoplasms Group, Cancer Research Program, IMIM-Hospital del Mar, Barcelona, Spain
| | - Eva Gimeno
- Hematology Department, Hospital del Mar-IMIM, Barcelona, Spain.,Applied Clinical Research in Hematological Malignances, Cancer Research Program, IMIM-Hospital del Mar, Barcelona, Spain
| | - Eugènia Abella
- Hematology Department, Hospital del Mar-IMIM, Barcelona, Spain.,Applied Clinical Research in Hematological Malignances, Cancer Research Program, IMIM-Hospital del Mar, Barcelona, Spain
| | - Pau Abrisqueta
- Hematology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Francesc Bosch
- Hematology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - José Yélamos
- Immunology Laboratory, Pathology Department, Hospital del Mar, Barcelona, Spain
| | - Ana Ferrer
- Molecular Cytogenetics Laboratory, Hematological Cytology Laboratory, Pathology Department, Hospital del Mar, Barcelona, Spain.,Translational Research on Hematological Neoplasms Group, Cancer Research Program, IMIM-Hospital del Mar, Barcelona, Spain
| | - Miguel López-Botet
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain.,University Pompeu Fabra (UPF), Barcelona, Spain
| | - Blanca Espinet
- Molecular Cytogenetics Laboratory, Hematological Cytology Laboratory, Pathology Department, Hospital del Mar, Barcelona, Spain.,Translational Research on Hematological Neoplasms Group, Cancer Research Program, IMIM-Hospital del Mar, Barcelona, Spain
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16
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Blanco G, Puiggros A, Sherry B, Nonell L, Calvo X, Puigdecanet E, Chiu PY, Kieso Y, Ferrer G, Palacios F, Arnal M, Rodríguez-Rivera M, Gimeno E, Abella E, Rai KR, Abrisqueta P, Bosch F, Calon A, Ferrer A, Chiorazzi N, Espinet B. Chronic lymphocytic leukemia-like monoclonal B-cell lymphocytosis exhibits an increased inflammatory signature that is reduced in early-stage chronic lymphocytic leukemia. Exp Hematol 2021; 95:68-80. [PMID: 33421548 DOI: 10.1016/j.exphem.2020.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 11/16/2022]
Abstract
Several studies in chronic lymphocytic leukemia (CLL) patients have reported impaired immune cell functions, which contribute to tumor evasion and disease progression. However, studies on CLL-like monoclonal B-cell lymphocytosis (MBL) are scarce. In the study described here, we characterized the immune environment in 62 individuals with clinical MBL, 56 patients with early-stage CLL, and 31 healthy controls. Gene expression arrays and quantitative reverse transcription polymerase chain reaction were performed on RNA from CD4+ peripheral blood cells; serum cytokines were measured with immunoassays; and HLA-DR expression on circulating monocytes, as well as the percentages of Th1, cytotoxic, exhausted, and effector CD4+ T cells, were evaluated by flow cytometry. In addition, cell cultures of clonal B cells and CD14-enriched or -depleted cell fractions were performed. Strikingly, MBL and early-stage CLL differed in pro-inflammatory signatures. An increased inflammatory drive orchestrated mainly by monocytes was identified in MBL, which exhibited enhanced phagocytosis, pattern recognition receptors, interleukin-8 (IL8), HMGB1, and acute response signaling pathways and increased pro-inflammatory cytokines (in particular IL8, interferon γ [IFNγ], and tumor necrosis factor α). This inflammatory signature was diminished in early-stage CLL (reduced IL8 and IFNγ levels, IL8 signaling pathway, and monocytic HLA-DR expression compared with MBL), especially in those patients with mutations in IGHV genes. Additionally, CD4+ T cells of MBL and early-stage CLL exhibited a similar upregulation of Th1 and cytotoxic genes and expanded CXCR3+ and perforin+ CD4+ T cells, as well as PD1+ CD4+ T cells, compared with controls. Cell culture assays disclosed tumor-supporting effects of monocytes similarly observed in MBL and early-stage CLL. These novel findings reveal differences in the inflammatory environment between MBL and CLL, highlighting an active role for antigen stimulation in the very early stages of the disease, potentially related to malignant B-cell transformation.
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Affiliation(s)
- Gonzalo Blanco
- Laboratori de Citogenètica Molecular, Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, Barcelona, Spain; Grup de Recerca Translacional en Neoplàsies Hematològiques, Cancer Research Program, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Anna Puiggros
- Laboratori de Citogenètica Molecular, Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, Barcelona, Spain; Grup de Recerca Translacional en Neoplàsies Hematològiques, Cancer Research Program, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Barbara Sherry
- Center for Immunology and Inflammation, The Feinstein Institute for Medical Research, Manhasset, NY; Department of Medicine, Hofstra Northwell School of Medicine, Hempstead, NY; Department of Molecular Medicine, Hofstra Northwell School of Medicine, Hempstead, NY
| | | | - Xavier Calvo
- Laboratori de Citogenètica Molecular, Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, Barcelona, Spain; Grup de Recerca Translacional en Neoplàsies Hematològiques, Cancer Research Program, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | | | - Pui Yan Chiu
- Center for Immunology and Inflammation, The Feinstein Institute for Medical Research, Manhasset, NY
| | - Yasmine Kieso
- Karches Center for Oncology Research, The Feinstein Institute for Medical Research, Manhasset, NY
| | - Gerardo Ferrer
- Karches Center for Oncology Research, The Feinstein Institute for Medical Research, Manhasset, NY
| | - Florencia Palacios
- Karches Center for Oncology Research, The Feinstein Institute for Medical Research, Manhasset, NY
| | | | - María Rodríguez-Rivera
- Laboratori de Citogenètica Molecular, Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, Barcelona, Spain; Grup de Recerca Translacional en Neoplàsies Hematològiques, Cancer Research Program, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Eva Gimeno
- Servei d'Hematologia, Hospital del Mar-IMIM, Barcelona, Spain; Grup de Recerca Clínica Aplicada en Neoplàsies Hematològiques, Cancer Research Program, IMIM-Hospital del Mar, Barcelona, Spain
| | - Eugènia Abella
- Servei d'Hematologia, Hospital del Mar-IMIM, Barcelona, Spain; Grup de Recerca Clínica Aplicada en Neoplàsies Hematològiques, Cancer Research Program, IMIM-Hospital del Mar, Barcelona, Spain
| | - Kanti R Rai
- Department of Medicine, Hofstra Northwell School of Medicine, Hempstead, NY; Karches Center for Oncology Research, The Feinstein Institute for Medical Research, Manhasset, NY
| | - Pau Abrisqueta
- Servei d'Hematologia, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Francesc Bosch
- Servei d'Hematologia, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Alexandre Calon
- Laboratori de Recerca Translacional en Microambient Tumoral, Cancer Research Program, IMIM, Barcelona, Spain
| | - Ana Ferrer
- Laboratori de Citogenètica Molecular, Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, Barcelona, Spain; Grup de Recerca Translacional en Neoplàsies Hematològiques, Cancer Research Program, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Nicholas Chiorazzi
- Department of Medicine, Hofstra Northwell School of Medicine, Hempstead, NY; Department of Molecular Medicine, Hofstra Northwell School of Medicine, Hempstead, NY; Karches Center for Oncology Research, The Feinstein Institute for Medical Research, Manhasset, NY
| | - Blanca Espinet
- Laboratori de Citogenètica Molecular, Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, Barcelona, Spain; Grup de Recerca Translacional en Neoplàsies Hematològiques, Cancer Research Program, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain.
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Almanza-Aguilera E, Hernáez Á, Corella D, Sanllorente A, Ros E, Portolés O, Valussi J, Estruch R, Coltell O, Subirana I, Canudas S, Razquin C, Blanchart G, Nonell L, Fitó M, Castañer O. Cancer Signaling Transcriptome Is Upregulated in Type 2 Diabetes Mellitus. J Clin Med 2020; 10:jcm10010085. [PMID: 33383630 PMCID: PMC7795776 DOI: 10.3390/jcm10010085] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/18/2020] [Accepted: 12/25/2020] [Indexed: 12/14/2022] Open
Abstract
We aimed to explore the differences in the whole transcriptome of peripheral blood mononuclear cells between elderly individuals with and without type 2 diabetes (T2D). We conducted a microarray-based transcriptome analysis of 19 individuals with T2D and 15 without. Differentially expressed genes according to linear models were submitted to the Ingenuity Pathway Analysis system to conduct a functional enrichment analysis. We established that diseases, biological functions, and canonical signaling pathways were significantly associated with T2D patients when their logarithms of Benjamini–Hochberg-adjusted p-value were >1.30 and their absolute z-scores were >2.0 (≥2.0 meant “upregulation” and ≤ −2.0 “downregulation”). Cancer signaling pathways were the most upregulated ones in T2D (z-score = 2.63, −log(p-value) = 32.3; 88.5% (n = 906) of the total differentially expressed genes located in these pathways). In particular, integrin (z-score = 2.52, −log(p-value) = 2.03) and paxillin (z-score = 2.33, −log(p-value) = 1.46) signaling pathways were predicted to be upregulated, whereas the Rho guanosine diphosphate (Rho-GDP) dissociation inhibitor signaling pathway was predicted to be downregulated in T2D individuals (z-score = −2.14, −log(p-value) = 2.41). Our results suggest that, at transcriptional expression level, elderly individuals with T2D present an increased activation of signaling pathways related to neoplastic processes, T-cell activation and migration, and inflammation.
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Affiliation(s)
- Enrique Almanza-Aguilera
- Cardiovascular Risk and Nutrition Research Group, Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain; (E.A.-A.); (A.S.); (J.V.); (G.B.); (M.F.)
- Centro de Investigación Biomédica en Red Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, 08921 Santa Coloma de Gramanet, Spain
| | - Álvaro Hernáez
- Cardiovascular Risk, Nutrition and Aging Research Unit, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain; (Á.H.); (R.E.)
- Blanquerna School of Life Sciences, Universitat Ramón Llull, 08025 Barcelona, Spain
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.C.); (E.R.); (O.P.); (O.C.); (S.C.); (C.R.)
| | - Dolores Corella
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.C.); (E.R.); (O.P.); (O.C.); (S.C.); (C.R.)
- Department of Preventive Medicine, University of Valencia, 46010 Valencia, Spain
| | - Albert Sanllorente
- Cardiovascular Risk and Nutrition Research Group, Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain; (E.A.-A.); (A.S.); (J.V.); (G.B.); (M.F.)
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.C.); (E.R.); (O.P.); (O.C.); (S.C.); (C.R.)
| | - Emilio Ros
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.C.); (E.R.); (O.P.); (O.C.); (S.C.); (C.R.)
- Department of Internal Medicine, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain
| | - Olga Portolés
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.C.); (E.R.); (O.P.); (O.C.); (S.C.); (C.R.)
- Department of Preventive Medicine, University of Valencia, 46010 Valencia, Spain
| | - Julieta Valussi
- Cardiovascular Risk and Nutrition Research Group, Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain; (E.A.-A.); (A.S.); (J.V.); (G.B.); (M.F.)
| | - Ramon Estruch
- Cardiovascular Risk, Nutrition and Aging Research Unit, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain; (Á.H.); (R.E.)
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.C.); (E.R.); (O.P.); (O.C.); (S.C.); (C.R.)
- Department of Internal Medicine, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain
| | - Oscar Coltell
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.C.); (E.R.); (O.P.); (O.C.); (S.C.); (C.R.)
- Department of Computer Languages and Systems, University Jaume I, 12071 Castellon, Spain
| | - Isaac Subirana
- Cardiovascular Epidemiology and Genetics Research Group, Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain;
- Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28009 Madrid, Spain
| | - Silvia Canudas
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.C.); (E.R.); (O.P.); (O.C.); (S.C.); (C.R.)
- Human Nutrition Department, Hospital Universitari Sant Joan, Institut d’Investigació Sanitària Pere Virgili, University Rovira i Virgili, 43204 Reus, Spain
| | - Cristina Razquin
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.C.); (E.R.); (O.P.); (O.C.); (S.C.); (C.R.)
- Department of Preventive Medicine and Public Health, IdiSNA, Navarra Institute for Health Research, University of Navarra, 31008 Pamplona, Spain
| | - Gemma Blanchart
- Cardiovascular Risk and Nutrition Research Group, Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain; (E.A.-A.); (A.S.); (J.V.); (G.B.); (M.F.)
| | - Lara Nonell
- Microarrays Analysis Service, Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain;
| | - Montserrat Fitó
- Cardiovascular Risk and Nutrition Research Group, Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain; (E.A.-A.); (A.S.); (J.V.); (G.B.); (M.F.)
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.C.); (E.R.); (O.P.); (O.C.); (S.C.); (C.R.)
| | - Olga Castañer
- Cardiovascular Risk and Nutrition Research Group, Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain; (E.A.-A.); (A.S.); (J.V.); (G.B.); (M.F.)
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain; (D.C.); (E.R.); (O.P.); (O.C.); (S.C.); (C.R.)
- Correspondence: ; Tel.: +34-933160705; Fax: +34-933160720
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Bustamante M, Hernandez‐Ferrer C, Tewari A, Sarria Y, Harrison G, Puigdecanet E, Nonell L, Kang W, Friedländer M, Estivill X, González J, Nieuwenhuijsen M, Young A. A study into how ultraviolet radiation from the sun effects genes in the skin. Br J Dermatol 2020. [DOI: 10.1111/bjd.19071] [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: 11/28/2022]
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Bustamante M, Hernandez‐Ferrer C, Tewari A, Sarria Y, Harrison G, Puigdecanet E, Nonell L, Kang W, Friedländer M, Estivill X, González J, Nieuwnhuijsen M, Young A. 太阳紫外线辐射如何影响皮肤基因的研究. Br J Dermatol 2020. [DOI: 10.1111/bjd.19083] [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: 11/27/2022]
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Segura S, Gadea A, Nonell L, Andrades E, Sánchez S, Pujol R, Hernández-Muñoz I, Toll A. Identification of differentially expressed genes in actinic keratosis samples treated with ingenol mebutate gel. PLoS One 2020; 15:e0232146. [PMID: 32413042 PMCID: PMC7228095 DOI: 10.1371/journal.pone.0232146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 12/18/2019] [Accepted: 04/07/2020] [Indexed: 12/22/2022] Open
Abstract
Actinic keratosis is a common skin disease that may progress to invasive squamous cell carcinoma if left untreated. Ingenol mebutate has demonstrated efficacy in field treatment of actinic keratosis. However, molecular mechanisms on ingenol mebutate response are not yet fully understood. In this study, we evaluated the gene expression profiles of actinic keratosis lesions before and after treatment with ingenol mebutate using microarray technology. Actinic keratoses on face/scalp of 15 immunocompetent patients were identified and evaluated after treatment with topical ingenol mebutate gel 0.015%, applied once daily for 3 consecutive days. Diagnostic and clearance of lesions was determined by clinical, dermoscopic, and reflectance confocal microscopy criteria. Lesional and non-lesional skin biopsies were subjected to gene expression analysis profiled by Affymetrix microarray. Differentially expressed genes were identified, and enrichment analyses were performed using STRING database. At 8 weeks post-treatment, 60% of patients responded to ingenol mebutate therapy, achieving complete clearance in 40% of cases. A total of 128 differentially expressed genes were identified following treatment, and downregulated genes (114 of 128) revealed changes in pathways important to epidermal development, keratinocyte differentiation and cornification. In responder patients, 388 downregulated genes (of 450 differentially expressed genes) were also involved in development/differentiation of the epidermis, and immune system-related pathways, such as cytokine and interleukin signaling. Cluster analysis revealed two relevant clusters showing upregulated profile patterns in pre-treatment actinic keratoses of responders, as compared to non-responders. Again, differentially expressed genes were mainly associated with cornification, keratinization and keratinocyte differentiation. Overall, the present study provides insight into the gene expression profile of actinic keratoses after treatment with ingenol mebutate, as well as identification of genetic signatures that could predict treatment response.
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Affiliation(s)
- Sonia Segura
- Department of Dermatology, Hospital del Mar, Parc de Salut Mar, Barcelona, Spain
| | - Alejandra Gadea
- Group of Inflamatory and Neoplasic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Centre National de la Recherche Scientifique (CNRS), Centre de Recherche Paul Pascal (CRPP), Université de Bordeaux, Pessac, France
| | - Lara Nonell
- MARGenomics, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Evelyn Andrades
- Group of Inflamatory and Neoplasic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Silvia Sánchez
- Group of Inflamatory and Neoplasic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Ramon Pujol
- Department of Dermatology, Hospital del Mar, Parc de Salut Mar, Barcelona, Spain
| | - Inmaculada Hernández-Muñoz
- Group of Inflamatory and Neoplasic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Agustí Toll
- Department of Dermatology, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
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Almanza-Aguilera E, Hernáez A, Corella D, Aguayo DM, Ros E, Portolés O, Valussi J, Estruch R, Coltell O, Subirana I, Salas-Salvadó J, Ruiz-Canela M, de la Torre R, Nonell L, Fitó M, Castañer O. Transcriptional response to a Mediterranean diet intervention exerts a modulatory effect on neuroinflammation signaling pathway. Nutr Neurosci 2020; 25:256-265. [PMID: 32290787 DOI: 10.1080/1028415x.2020.1749334] [Citation(s) in RCA: 2] [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] [Indexed: 12/20/2022]
Abstract
Background: The Traditional Mediterranean Diet (TMD) is known to have beneficial effects on several chronic diseases. However, data concerning the whole transcriptome modulation of the TMD are scarce.Objective: We aimed to explore the effects of the TMD on the whole transcriptome of individuals at high cardiovascular risk.Methods: Thirty-four participants at high cardiovascular risk were randomly assigned to a TMD enriched with extra-virgin olive oil (TMD + VOO), mixed nuts (TMD + Nuts), or a control diet based on low-fat diet recommendations. A microarray analysis in circulating peripheral blood mononuclear cells of the participants was conducted before and after 3 months of the intervention. The association of changes in gene expression was modeled into canonical pathways by conducting an untargeted functional analysis with the Ingenuity Pathway Analysis® (IPA). Effects were considered significant when the absolute z-score values were ≥2.0 and the logarithm P (adjusted by the Benjamini-Hochberg procedure [BH]) values were ≥1.30.Results: According to IPA, interventions with TMD + Nuts, TMD + VOO, and control diet downregulated neuroinflammation, triggering receptor expressed on myeloid cells 1 , and cholecystokinin/gastrin-mediated signaling pathways, respectively. The gene expression among these pathways included cytokines, T-cell activation receptors, nuclear factor kappa β/inflammasome components, pro-inflammatory enzymes and cell cycle regulators.Conclusion: The current findings suggest that the TMD enriched with mixed nuts or VOO downregulate transcriptomic pathways, including those related to neuroinflammation, which could influence development of neurodegenerative diseases. Our data should be corroborated in other tissue cells, such as neurons and glial cells. The PREDIMED trial was registered at https://www.controlled-trials.com (ISRCTN35739639).
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Affiliation(s)
- Enrique Almanza-Aguilera
- Cardiovascular Risk and Nutrition research group (CARIN), Hospital del Mar Research Institute (IMIM) Barcelona, Spain.,Centro de Investigación Biomédica en Red Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Madrid, Spain.,Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, Santa Coloma de Gramenet, Spain
| | - Alvaro Hernáez
- Blanquerna School of Life Sciences, Universitat Ramón Llull, Barcelona, Spain.,Cardiovascular Risk, Nutrition and Aging Research Unit, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Dolores Corella
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III Madrid, Spain.,Department of Preventive Medicine, University of Valencia, Valencia, Spain
| | - Daniel Muñoz Aguayo
- Cardiovascular Risk and Nutrition research group (CARIN), Hospital del Mar Research Institute (IMIM) Barcelona, Spain.,Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III Madrid, Spain
| | - Emilio Ros
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III Madrid, Spain.,Department of Internal Medicine, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Olga Portolés
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III Madrid, Spain.,Department of Preventive Medicine, University of Valencia, Valencia, Spain
| | - Julieta Valussi
- Cardiovascular Risk and Nutrition research group (CARIN), Hospital del Mar Research Institute (IMIM) Barcelona, Spain
| | - Ramon Estruch
- Cardiovascular Risk, Nutrition and Aging Research Unit, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III Madrid, Spain.,Department of Internal Medicine, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Oscar Coltell
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III Madrid, Spain.,Department of Computer Science and Languages, University Jaume I, Castellon, Spain
| | - Isaac Subirana
- Cardiovascular Epidemiology and Genetics Research Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain.,Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Jordi Salas-Salvadó
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III Madrid, Spain.,Human Nutrition Department, Hospital Universitari Sant Joan, Institut d'Investigació Sanitària Pere Virgili, University Rovira i Virgili, Reus, Spain
| | - Miguel Ruiz-Canela
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III Madrid, Spain.,Department of Preventive Medicine and Public Health, University of Navarra-Institute of Health Research of Navarra, Pamplona, Spain
| | - Rafael de la Torre
- Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III Madrid, Spain.,Integrative Pharmacology and Systems Neuroscience research group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra (CEXS-UPF), Barcelona, Spain
| | - Lara Nonell
- Microarrays analysis service, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Montserrat Fitó
- Cardiovascular Risk and Nutrition research group (CARIN), Hospital del Mar Research Institute (IMIM) Barcelona, Spain.,Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III Madrid, Spain
| | - Olga Castañer
- Cardiovascular Risk and Nutrition research group (CARIN), Hospital del Mar Research Institute (IMIM) Barcelona, Spain.,Centro de Investigación Biomédica en Red Fisiopatologia de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III Madrid, Spain
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22
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Bustamante M, Hernandez-Ferrer C, Tewari A, Sarria Y, Harrison GI, Puigdecanet E, Nonell L, Kang W, Friedländer MR, Estivill X, González JR, Nieuwenhuijsen M, Young AR. Dose and time effects of solar-simulated ultraviolet radiation on the in vivo human skin transcriptome. Br J Dermatol 2019; 182:1458-1468. [PMID: 31529490 PMCID: PMC7318624 DOI: 10.1111/bjd.18527] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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] [Accepted: 09/10/2019] [Indexed: 12/18/2022]
Abstract
Background Terrestrial ultraviolet (UV) radiation causes erythema, oxidative stress, DNA mutations and skin cancer. Skin can adapt to these adverse effects by DNA repair, apoptosis, keratinization and tanning. Objectives To investigate the transcriptional response to fluorescent solar‐simulated radiation (FSSR) in sun‐sensitive human skin in vivo. Methods Seven healthy male volunteers were exposed to 0, 3 and 6 standard erythemal doses (SED). Skin biopsies were taken at 6 h and 24 h after exposure. Gene and microRNA expression were quantified with next generation sequencing. A set of candidate genes was validated by quantitative polymerase chain reaction (qPCR); and wavelength dependence was examined in other volunteers through microarrays. Results The number of differentially expressed genes increased with FSSR dose and decreased between 6 and 24 h. Six hours after 6 SED, 4071 genes were differentially expressed, but only 16 genes were affected at 24 h after 3 SED. Genes for apoptosis and keratinization were prominent at 6 h, whereas inflammation and immunoregulation genes were predominant at 24 h. Validation by qPCR confirmed the altered expression of nine genes detected under all conditions; genes related to DNA repair and apoptosis; immunity and inflammation; pigmentation; and vitamin D synthesis. In general, candidate genes also responded to UVA1 (340–400 nm) and/or UVB (300 nm), but with variations in wavelength dependence and peak expression time. Only four microRNAs were differentially expressed by FSSR. Conclusions The UV radiation doses of this acute study are readily achieved daily during holidays in the sun, suggesting that the skin transcriptional profile of ‘typical’ holiday makers is markedly deregulated. What's already known about this topic? The skin's transcriptional profile underpins its adverse (i.e. inflammation) and adaptive molecular, cellular and clinical responses (i.e. tanning, hyperkeratosis) to solar ultraviolet radiation. Few studies have assessed microRNA and gene expression in vivo in humans, and there is a lack of information on dose, time and waveband effects.
What does this study add? Acute doses of fluorescent solar‐simulated radiation (FSSR), of similar magnitude to those received daily in holiday situations, markedly altered the skin's transcriptional profiles. The number of differentially expressed genes was FSSR‐dose‐dependent, reached a peak at 6 h and returned to baseline at 24 h. The initial transcriptional response involved apoptosis and keratinization, followed by inflammation and immune modulation. In these conditions, microRNA expression was less affected than gene expression.
Linked Comment:Hart. Br J Dermatol 2020; 182:1328–1329. Plain language summary available online Respond to this article
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Affiliation(s)
- M Bustamante
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - C Hernandez-Ferrer
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.,Computational Health Informatics Program (CHIP), Boston Children's Hospital, Boston, MA, U.S.A
| | - A Tewari
- King's College London, St John's Institute of Dermatology, London, U.K
| | - Y Sarria
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - G I Harrison
- King's College London, St John's Institute of Dermatology, London, U.K
| | - E Puigdecanet
- Servei d'Anàlisi de Microarrays, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - L Nonell
- Servei d'Anàlisi de Microarrays, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - W Kang
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - M R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - X Estivill
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.,Genetics Program, Sidra Medical Center, Al Rayyan Municipality, Qatar
| | - J R González
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - M Nieuwenhuijsen
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - A R Young
- King's College London, St John's Institute of Dermatology, London, U.K
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23
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Oliva J, Larque A, Marti C, Bodalo‐Torruella M, Nonell L, Nadal A, Castillo P, Sieira R, Ferrer A, Garcia‐Diez E, Alos L. Oral premalignant lesions of smokers and non‐smokers show similar carcinogenic pathways and outcomes. A clinicopathological and molecular comparative analysis. J Oral Pathol Med 2019; 50:280-286. [DOI: 10.1111/jop.12864] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/04/2019] [Accepted: 04/15/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Jorge Oliva
- Department of Pathology, Hospital Clínic, IDIBAPS University of Barcelona Barcelona Spain
| | - Ana‐Belen Larque
- Department of Pathology, Hospital Clínic, IDIBAPS University of Barcelona Barcelona Spain
| | - Carles Marti
- Department of Maxillofacial Surgery Hospital Clínic Barcelona Spain
| | - Marta Bodalo‐Torruella
- Microarray Analysis Service Institut Hospital del Mar d’InvestigacionsMèdiques (IMIM) Barcelona Spain
| | - Lara Nonell
- Microarray Analysis Service Institut Hospital del Mar d’InvestigacionsMèdiques (IMIM) Barcelona Spain
| | - Alfons Nadal
- Department of Pathology, Hospital Clínic, IDIBAPS University of Barcelona Barcelona Spain
| | - Paola Castillo
- Department of Pathology, Hospital Clínic, IDIBAPS University of Barcelona Barcelona Spain
| | - Ramón Sieira
- Department of Maxillofacial Surgery Hospital Clínic Barcelona Spain
| | - Ada Ferrer
- Department of Maxillofacial Surgery Hospital Clínic Barcelona Spain
| | - Eloy Garcia‐Diez
- Department of Maxillofacial Surgery Hospital Clínic Barcelona Spain
| | - Llucia Alos
- Department of Pathology, Hospital Clínic, IDIBAPS University of Barcelona Barcelona Spain
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24
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Hardy-Werbin M, Rocha P, Arpi O, Taus Á, Nonell L, Durán X, Villanueva X, Joseph-Pietras D, Nolan L, Danson S, Griffiths R, Lopez-Botet M, Rovira A, Albanell J, Ottensmeier C, Arriola E. Serum cytokine levels as predictive biomarkers of benefit from ipilimumab in small cell lung cancer. Oncoimmunology 2019; 8:e1593810. [PMID: 31069160 DOI: 10.1080/2162402x.2019.1593810] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [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: 12/19/2018] [Revised: 02/22/2019] [Accepted: 02/28/2019] [Indexed: 01/22/2023] Open
Abstract
Background. Immunotherapy has shown efficacy in small cell lung cancer (SCLC), but only a subset of patients benefits. Surrogate biomarkers are urgently needed. Our aim was to evaluate serum Th1, Th2, and proinflammatory cytokines in two cohorts of SCLC patients before and during treatment with chemotherapy with or without ipilimumab and to correlate them with survival. Patients and methods. Two cohorts of SCLC patients were studied: patients treated with chemotherapy (n = 47), and patients treated with chemotherapy plus ipilimumab (n = 37). Baseline, on-treatment and after-treatment serum samples were evaluated for the presence of IL-1beta, IL-2, IL-4, IL-5, IL-6, IL-8, IL-10, IFN-gamma, TNF-alpha, GM-CSF, and Mip-1alpha using a Luminex assay. Differential changes in cytokines between cohorts were analyzed. Associations between cytokine levels and their changes with overall survival were evaluated. Results. Patients treated with ipilimumab showed a global increase of all cytokines after treatment initiation. A high level of IL-8 at baseline was associated with worse prognosis regardless of treatment. Baseline increased IL-2 levels predicted sensitivity to ipilimumab, while high IL-6 and TNF-alpha predicted resistance. An on-treatment increase in IL-4 levels in patients treated with immune-chemotherapy was associated with a better overall survival. Conclusions. The addition of ipilimumab to standard chemotherapy in SCLC modulates the serum levels of cytokines. Baseline levels and their change over time relate to overall survival. Blood-based biomarkers are convenient for patients, and our results support prospective validation of cytokines as predictive biomarkers for ipilimumab in SCLC.
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Affiliation(s)
- Max Hardy-Werbin
- Cancer Research Program, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Pedro Rocha
- Medical Oncology Department, Hospital del Mar-CIBERONC, Barcelona, Spain
| | - Oriol Arpi
- Cancer Research Program, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Barcelona, Spain
| | - Álvaro Taus
- Medical Oncology Department, Hospital del Mar-CIBERONC, Barcelona, Spain
| | - Lara Nonell
- Microarrays analysis service, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Barcelona, Spain
| | - Xavier Durán
- Statistics department, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Barcelona, Spain
| | - Xavier Villanueva
- Medical Oncology Department, Hospital del Mar-CIBERONC, Barcelona, Spain
| | | | - Luke Nolan
- Medical Oncology Department, University Hospital Southampton, Southampton, UK
| | - Sarah Danson
- Sheffield Experimental Cancer Medicine Centre, Weston Park Hospital, Sheffield, UK
| | | | - Miguel Lopez-Botet
- Immunology unit, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Ana Rovira
- Cancer Research Program, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Barcelona, Spain.,Medical Oncology Department, Hospital del Mar-CIBERONC, Barcelona, Spain
| | - Joan Albanell
- Cancer Research Program, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Barcelona, Spain.,Medical Oncology Department, Hospital del Mar-CIBERONC, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Christian Ottensmeier
- NIHR Experimental Cancer Medicine Centre, Southampton, UK.,Cancer Science Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Edurne Arriola
- Cancer Research Program, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Barcelona, Spain.,Medical Oncology Department, Hospital del Mar-CIBERONC, Barcelona, Spain
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25
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García-Díez I, Hernández-Muñoz I, Hernández-Ruiz E, Nonell L, Puigdecanet E, Bódalo-Torruella M, Andrades E, Pujol RM, Toll A. Transcriptome and cytogenetic profiling analysis of matched in situ/invasive cutaneous squamous cell carcinomas from immunocompetent patients. Genes Chromosomes Cancer 2019; 58:164-174. [DOI: 10.1002/gcc.22712] [Citation(s) in RCA: 13] [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: 02/07/2018] [Revised: 11/01/2018] [Accepted: 11/22/2018] [Indexed: 12/17/2022] Open
Affiliation(s)
- Irene García-Díez
- Department of Dermatology; Hospital del Mar, Universitat Autònoma de Barcelona (UAB); Barcelona Spain
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Inmaculada Hernández-Muñoz
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Eugenia Hernández-Ruiz
- Department of Dermatology; Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB); Barcelona Spain
| | - Lara Nonell
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Eulàlia Puigdecanet
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Marta Bódalo-Torruella
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Evelyn Andrades
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Ramon M. Pujol
- Department of Dermatology; Hospital del Mar, Universitat Autònoma de Barcelona (UAB); Barcelona Spain
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
| | - Agustí Toll
- Department of Dermatology; Hospital del Mar, Universitat Autònoma de Barcelona (UAB); Barcelona Spain
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute); Barcelona Spain
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26
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Ramirez J, Font Pous A, Garcia-Donas J, Perez Valderrama B, Aguirre Egaña I, Nonell L, Ruiz de Porras Fontdevila V, Mallo M, Balañá D, Virizuela J, Anido U, Llorente Ostiategui M, Gonzalez del Alba Baamonde M, Lainez N, Mellado B, Climent Duran M, Bellmunt J. Differential gene expression profiles in poor vs good responders to maintenance vinflunine in patients (p) with advanced urothelial carcinoma (aUC): Preliminary results of biomarker analyses from the MAJA trial (SOGUG 2011/02). Ann Oncol 2018. [DOI: 10.1093/annonc/mdy269.126] [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: 11/12/2022] Open
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27
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Pascual-Reguant L, Blanco E, Galan S, Le Dily F, Cuartero Y, Serra-Bardenys G, Di Carlo V, Iturbide A, Cebrià-Costa JP, Nonell L, de Herreros AG, Di Croce L, Marti-Renom MA, Peiró S. Lamin B1 mapping reveals the existence of dynamic and functional euchromatin lamin B1 domains. Nat Commun 2018; 9:3420. [PMID: 30143639 PMCID: PMC6109041 DOI: 10.1038/s41467-018-05912-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [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: 08/17/2017] [Accepted: 08/02/2018] [Indexed: 12/13/2022] Open
Abstract
Lamins (A/C and B) are major constituents of the nuclear lamina (NL). Structurally conserved lamina-associated domains (LADs) are formed by genomic regions that contact the NL. Lamins are also found in the nucleoplasm, with a yet unknown function. Here we map the genome-wide localization of lamin B1 in an euchromatin-enriched fraction of the mouse genome and follow its dynamics during the epithelial-to-mesenchymal transition (EMT). Lamin B1 associates with actively expressed and open euchromatin regions, forming dynamic euchromatin lamin B1-associated domains (eLADs) of about 0.3 Mb. Hi-C data link eLADs to the 3D organization of the mouse genome during EMT and correlate lamin B1 enrichment at topologically associating domain (TAD) borders with increased border strength. Having reduced levels of lamin B1 alters the EMT transcriptional signature and compromises the acquisition of mesenchymal traits. Thus, during EMT, the process of genome reorganization in mouse involves dynamic changes in eLADs.
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Affiliation(s)
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Silvia Galan
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Structural Genomic Group, CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - François Le Dily
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Yasmina Cuartero
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Structural Genomic Group, CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Gemma Serra-Bardenys
- Vall d'Hebron Institute of Oncology, 08035, Barcelona, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Valerio Di Carlo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Ane Iturbide
- Institute of Epigenetics and Stem Cells, D-81377, München, Germany
| | | | - Lara Nonell
- Servei d'Anàlisi de Microarrays Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Antonio García de Herreros
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- ICREA, Pg. Lluis Companys 23, Barcelona, Spain
| | - Marc A Marti-Renom
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
- Structural Genomic Group, CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
- ICREA, Pg. Lluis Companys 23, Barcelona, Spain
| | - Sandra Peiró
- Vall d'Hebron Institute of Oncology, 08035, Barcelona, Spain.
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28
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Giménez‐Arnau A, Curto‐Barredo L, Nonell L, Puigdecanet E, Yelamos J, Gimeno R, Rüberg S, Santamaria‐Babi L, Pujol R. Transcriptome analysis of severely active chronic spontaneous urticaria shows an overall immunological skin involvement. Allergy 2017; 72:1778-1790. [PMID: 28407332 DOI: 10.1111/all.13183] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2017] [Indexed: 02/02/2023]
Abstract
BACKGROUND The knowledge about chronic spontaneous urticaria (CSU) phenotypes is based on its clinical characteristics, associated comorbidities, course of the disease, and its response to the available effective drugs. Genotype expression and its further correlation with CSU phenotypes are still unknown. We describe the cutaneous transcriptome of patients suffering a severely active CSU refractory to antihistamine treatment. METHODS Through the bioinformatic analysis of the whole Human Genome with Oligo Microarrays and quantitative real-time polymerase chain reaction (qPCR), relevant genes expressed in nonlesional (NLS-CSU) and lesional skin (LS-CSU) and peripheral blood were identified in 20 patients suffering from severely active CSU and 10 healthy controls (HCs). RESULTS From 39 genes differentially expressed in NLS-CSU when compared with HCs, 31 (79.48%) were confirmed by qPCR corresponding to genes involved in epidermal homeostasis and dermal repair. From the analysis comparing LS-CSU with NLS-CSU, a selection of 142 genes was studied with qPCR, and 103 (72.53%) were confirmed. Differentially expressed genes in the phenomenon of wheal development are involved in a variety of biological functions as, epidermal differentiation, intracellular signal function, transcriptional factors cell cycle differentiation, inflammation, or coagulation. Differentially expressed genes that uniformly increase or decrease along the skin worsening until the wheal appearance is shown. CONCLUSION The skin of CSU patients with a severely active disease shows an overall immunological skin involvement showing a peculiar gene profile.
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Affiliation(s)
- A. Giménez‐Arnau
- Department of Dermatology Hospital del Mar IMIM Universitat Autònoma de Barcelona Barcelona Spain
| | - L. Curto‐Barredo
- Department of Dermatology Hospital del Mar IMIM Universitat Autònoma de Barcelona Barcelona Spain
| | - L. Nonell
- Microarray Analysis Service Institut Hospital del Mar d'Investigacions Mèdiques (IMIM) Barcelona Spain
| | - E. Puigdecanet
- Microarray Analysis Service Institut Hospital del Mar d'Investigacions Mèdiques (IMIM) Barcelona Spain
| | - J. Yelamos
- Immunology Department Institut Hospital del Mar d'Investigacions Mèdiques (IMIM) Barcelona Spain
| | - R. Gimeno
- Immunology Department Institut Hospital del Mar d'Investigacions Mèdiques (IMIM) Barcelona Spain
| | - S. Rüberg
- Microarray Analysis Service Milteny Biotec GmbH Teterow Germany
| | - L. Santamaria‐Babi
- Translational Immunology, Department of Physiology and Immunology Universitat de Barcelona Barcelona Spain
| | - R.M. Pujol
- Department of Dermatology Hospital del Mar IMIM Universitat Autònoma de Barcelona Barcelona Spain
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29
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Bustamante M, Hernandez-Ferrer C, Sarria Y, Harrison GI, Nonell L, Kang W, Friedländer MR, Estivill X, González JR, Nieuwenhuijsen M, Young AR. The acute effects of ultraviolet radiation on the blood transcriptome are independent of plasma 25OHD 3. Environ Res 2017; 159:239-248. [PMID: 28822308 DOI: 10.1016/j.envres.2017.07.045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/05/2017] [Accepted: 07/25/2017] [Indexed: 06/07/2023]
Abstract
The molecular basis of many health outcomes attributed to solar ultraviolet radiation (UVR) is unknown. We tested the hypothesis that they may originate from transcriptional changes in blood cells. This was determined by assessing the effect of fluorescent solar simulated radiation (FSSR) on the transcriptional profile of peripheral blood pre- and 6h, 24h and 48h post-exposure in nine healthy volunteers. Expression of 20 genes was down-regulated and one was up-regulated at 6h after FSSR. All recovered to baseline expression at 24h or 48h. These genes have been associated with immune regulation, cancer and blood pressure; health effects attributed to vitamin D via solar UVR exposure. Plasma 25-hydroxyvitamin D3 [25OHD3] levels increased over time after FSSR and were maximal at 48h. The increase was more pronounced in participants with low basal 25OHD3 levels. Mediation analyses suggested that changes in gene expression due to FSSR were independent of 25OHD3 and blood cell subpopulations.
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Affiliation(s)
- Mariona Bustamante
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.
| | - Carles Hernandez-Ferrer
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Yaris Sarria
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Graham I Harrison
- King's College London (KCL), St John's Institute of Dermatology, London, UK
| | - Lara Nonell
- Servei d'Anàlisi de Microarrays, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Wenjing Kang
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Xavier Estivill
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Juan R González
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Mark Nieuwenhuijsen
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Antony R Young
- King's College London (KCL), St John's Institute of Dermatology, London, UK.
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30
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De-Ugarte L, Serra-Vinardell J, Nonell L, Balcells S, Arnal M, Nogues X, Mellibovsky L, Grinberg D, Diez-Perez A, Garcia-Giralt N. Expression profiling of microRNAs in human bone tissue from postmenopausal women. Hum Cell 2017; 31:33-41. [PMID: 28933035 DOI: 10.1007/s13577-017-0181-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/18/2017] [Indexed: 12/13/2022]
Abstract
Bone tissue is composed of several cell types, which express their own microRNAs (miRNAs) that will play a role in cell function. The set of total miRNAs expressed in all cell types configures the specific signature of the bone tissue in one physiological condition. The aim of this study was to explore the miRNA expression profile of bone tissue from postmenopausal women. Tissue was obtained from trabecular bone and was analyzed in fresh conditions (n = 6). Primary osteoblasts were also obtained from trabecular bone (n = 4) and human osteoclasts were obtained from monocyte precursors after in vitro differentiation (n = 5). MicroRNA expression profiling was obtained for each sample by microarray and a global miRNA analysis was performed combining the data acquired in all the microarray experiments. From the 641 miRNAs detected in bone tissue samples, 346 (54%) were present in osteoblasts and/or osteoclasts. The other 46% were not identified in any of the bone cells analyzed. Intersection of osteoblast and osteoclast arrays identified 101 miRNAs shared by both cell types, which accounts for 30-40% of miRNAs detected in these cells. In osteoblasts, 266 miRNAs were detected, of which 243 (91%) were also present in the total bone array, representing 38% of all bone miRNAs. In osteoclasts, 340 miRNAs were detected, of which 196 (58%) were also present in the bone tissue array, representing 31% of all miRNAs detected in total bone. These analyses provide an overview of miRNAs expressed in bone tissue, broadening our knowledge in the microRNA field.
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Affiliation(s)
- Laura De-Ugarte
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, C/Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Jenny Serra-Vinardell
- Department of Genetics, Microbiology and Statistics, Facultat de Biologia, Universitat de Barcelona, IBUB, IRSJD, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain
| | - Lara Nonell
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Susana Balcells
- Department of Genetics, Microbiology and Statistics, Facultat de Biologia, Universitat de Barcelona, IBUB, IRSJD, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain
| | - Magdalena Arnal
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Xavier Nogues
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, C/Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Leonardo Mellibovsky
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, C/Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Facultat de Biologia, Universitat de Barcelona, IBUB, IRSJD, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain
| | - Adolfo Diez-Perez
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, C/Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Natalia Garcia-Giralt
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, C/Dr. Aiguader 88, 08003, Barcelona, Spain.
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31
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Garcia-Elias A, Alloza L, Puigdecanet E, Nonell L, Tajes M, Curado J, Enjuanes C, Díaz O, Bruguera J, Martí-Almor J, Comín-Colet J, Benito B. Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs. Sci Rep 2017; 7:7725. [PMID: 28798363 PMCID: PMC5552704 DOI: 10.1038/s41598-017-08134-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 07/05/2017] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) have emerged as promising biomarkers of disease. Their potential use in clinical practice requires standardized protocols with very low miRNA concentrations, particularly in plasma samples. Here we tested the most appropriate method for miRNA quantification and validated the performance of a hybridization platform using lower amounts of starting RNA. miRNAs isolated from human plasma and from a reference sample were quantified using four platforms and profiled with hybridization arrays and RNA sequencing (RNA-seq). Our results indicate that the Infinite® 200 PRO Nanoquant and Nanodrop 2000 spectrophotometers magnified the miRNA concentration by detecting contaminants, proteins, and other forms of RNA. The Agilent 2100 Bioanalyzer PicoChip and SmallChip gave valuable information on RNA profile but were not a reliable quantification method for plasma samples. The Qubit® 2.0 Fluorometer provided the most accurate quantification of miRNA content, although RNA-seq confirmed that only ~58% of small RNAs in plasma are true miRNAs. On the other hand, reducing the starting RNA to 70% of the recommended amount for miRNA profiling with arrays yielded results comparable to those obtained with the full amount, whereas a 50% reduction did not. These findings provide important clues for miRNA determination in human plasma samples.
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Affiliation(s)
- Anna Garcia-Elias
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.
| | - Leonor Alloza
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Eulàlia Puigdecanet
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Lara Nonell
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Marta Tajes
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Joao Curado
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra, C/Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Cristina Enjuanes
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.,Cardiology Department, Hospital del Mar, Passeig Marítim 25-29, 08003, Barcelona, Spain
| | - Oscar Díaz
- Cardiovascular Risk and Nutrition Group, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Jordi Bruguera
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.,Cardiology Department, Hospital del Mar, Passeig Marítim 25-29, 08003, Barcelona, Spain
| | - Julio Martí-Almor
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.,Cardiology Department, Hospital del Mar, Passeig Marítim 25-29, 08003, Barcelona, Spain
| | - Josep Comín-Colet
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.,Cardiology Department, Hospital del Mar, Passeig Marítim 25-29, 08003, Barcelona, Spain
| | - Begoña Benito
- Group of Biomedical Research in Heart Diseases, IMIM (Hospital del Mar Medical Research Institute), C/Doctor Aiguader 88, 08003, Barcelona, Spain.,Cardiology Department, Hospital del Mar, Passeig Marítim 25-29, 08003, Barcelona, Spain
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32
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Alonso S, Mayol X, Nonell L, Salvans S, Pascual M, Pera M. Peripheral blood leucocytes show differential expression of tumour progression-related genes in colorectal cancer patients who have a postoperative intra-abdominal infection: a prospective matched cohort study. Colorectal Dis 2017; 19:O115-O125. [PMID: 28214365 DOI: 10.1111/codi.13635] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/22/2016] [Indexed: 02/08/2023]
Abstract
AIM Anastomotic leak is associated with higher rates of recurrence after surgery for colorectal cancer. However, the mechanisms responsible are unknown. We hypothesized that the infection-induced inflammatory response may induce overexpression of tumour progression-related genes in immune cells. The aim was to investigate the effect of postoperative intra-abdominal infection on the gene expression patterns of peripheral blood leucocytes (PBL) after surgery for colorectal cancer. METHOD Prospective matched cohort study. Patients undergoing surgery for colorectal cancer were included. Patients who had anastomotic leak or intra-abdominal abscess were included in the infection group (n = 23) and matched with patients without complications for the control group (n = 23). PBL were isolated from postoperative blood samples. Total RNA was extracted and hybridized to the Affymetrix Human Gene 1.0 ST microarray. RESULTS Patients in the infection group displayed 162 upregulated genes and 146 downregulated genes with respect to the control group. Upregulated genes included examples coding for secreted cytokines involved in tumour growth and invasion (S100P, HGF, MMP8, MMP9, PDGFC, IL1R2). Infection also upregulated some proangiogenic genes (CEP55, TRPS1) and downregulated some inhibitors of angiogenesis (MME, ALOX15, CXCL10). Finally, some inhibitors (HP, ORM1, OLFM4, IRAK3) and activators (GNLY, PRF1, FGFBP2) of antitumour immunity were upregulated and downregulated, respectively, suggesting that the inflammatory environment caused by a postoperative infection favours immune evasion mechanisms of the tumour. CONCLUSION Analysis of PBL shows differential expression of certain tumour progression-related genes in colorectal cancer patients who have a postoperative intra-abdominal infection, which in turn may promote the growth of residual cancer cells to become recurrent tumours.
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Affiliation(s)
- S Alonso
- Section of Colon and Rectal Surgery, Department of Surgery, Hospital del Mar, Barcelona, Spain
| | - X Mayol
- Section of Colon and Rectal Surgery, Department of Surgery, Hospital del Mar, Barcelona, Spain
| | - L Nonell
- Microarray Analysis Service, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - S Salvans
- Section of Colon and Rectal Surgery, Department of Surgery, Hospital del Mar, Barcelona, Spain
| | - M Pascual
- Section of Colon and Rectal Surgery, Department of Surgery, Hospital del Mar, Barcelona, Spain
| | - M Pera
- Section of Colon and Rectal Surgery, Department of Surgery, Hospital del Mar, Barcelona, Spain
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33
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Companioni O, Sanz-Anquela JM, Pardo ML, Puigdecanet E, Nonell L, García N, Parra Blanco V, López C, Andreu V, Cuatrecasas M, Garmendia M, Gisbert JP, Gonzalez CA, Sala N. Gene expression study and pathway analysis of histological subtypes of intestinal metaplasia that progress to gastric cancer. PLoS One 2017; 12:e0176043. [PMID: 28441455 PMCID: PMC5404762 DOI: 10.1371/journal.pone.0176043] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 09/07/2016] [Accepted: 04/04/2017] [Indexed: 02/06/2023] Open
Abstract
Background Intestinal metaplasia (IM) is a precursor lesion that precedes gastric cancer (GC). There are two IM histological subtypes, complete (CIM) and incomplete (IIM), the latter having higher progression rates to GC. This study was aimed at analysing gene expression and molecular processes involved in the progression from normal mucosa to IM, and also from IM subtypes to GC. Methodology We used expression data to compare the transcriptome of healthy gastric mucosa to that of IM not progressing to GC, and the transcriptome of IM subtypes that had progressed to GC to those that did not progress. Some deregulated genes were validated and pathway analyses were performed. Results Comparison of IM subtypes that had progressed to GC with those that did not progress showed smaller differences in the expression profiles than the comparison of IM that did not progress with healthy mucosa. New transcripts identified in IM not progressing to GC included TRIM, TMEM, homeobox and transporter genes and SNORD116. Comparison to normal mucosa identified non tumoral Warburg effect and melatonin degradation as previously unreported processes involved in IM. Overexpressed antigen processing is common to both IM-subtypes progressing to GC, but IIM showed more over-expressed oncogenic genes and molecular processes than CIM. Conclusions There are greater differences in gene expression and molecular processes involved in the progression from normal healthy mucosa to IM than from IM to gastric cancer. While antigen processing is common in both IM-subtypes progressing to GC, more oncogenic processes are observed in the progression of IIM.
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Affiliation(s)
- Osmel Companioni
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Institut Català d’Oncologia, Barcelona, Spain
- * E-mail: (NS); (OC)
| | - José Miguel Sanz-Anquela
- Cancer Registry and Pathology Department, Hospital Universitario Príncipe de Asturias and Department of Medicine and Medical Specialties, Faculty of Medicine, University of Alcalá, Alcalá de Henares, Madrid, Spain
| | | | - Eulàlia Puigdecanet
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Lara Nonell
- Microarray Analysis Service, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Nadia García
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Institut Català d’Oncologia, Barcelona, Spain
| | - Verónica Parra Blanco
- Department of Histopathology, Hospital Universitario Gregorio Marañón, Madrid, Spain
| | - Consuelo López
- Department of Pathology, Hospital Universitario de la Princesa, Madrid, Spain
| | - Victoria Andreu
- Department of Gastroenterology, Hospital de Viladecans, Spain
| | - Miriam Cuatrecasas
- Department of Pathology, Hospital Clínic de Barcelona, Universitat de Barcelona, Biobanc Clinic IDIBAPS, Barcelona, Spain
| | - Maddi Garmendia
- Department of Pathology, and Department of Gastroenterology, Hospital Donostia/Instituto Biodonostia, Universidad del País Vasco (UPV/EHU), CIBEREHD, San Sebastián, Spain
| | - Javier P. Gisbert
- Gastroenterology Unit, Hospital Universitario de La Princesa and Instituto de Investigación Sanitaria Princesa (IIS-IP), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Carlos A. Gonzalez
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Institut Català d’Oncologia, Barcelona, Spain
| | - Núria Sala
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Institut Català d’Oncologia, Barcelona, Spain
- * E-mail: (NS); (OC)
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Nicolle D, Fabre M, Simon-Coma M, Gorse A, Kappler R, Nonell L, Mallo M, Haidar H, Déas O, Mussini C, Guettier C, Redon MJ, Brugières L, Ghigna MR, Fadel E, Galmiche-Rolland L, Chardot C, Judde JG, Armengol C, Branchereau S, Cairo S. Patient-derived mouse xenografts from pediatric liver cancer predict tumor recurrence and advise clinical management. Hepatology 2016; 64:1121-35. [PMID: 27115099 DOI: 10.1002/hep.28621] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/25/2016] [Accepted: 04/20/2016] [Indexed: 01/30/2023]
Abstract
UNLABELLED Identification of new treatments for relapsing pediatric cancer is an unmet clinical need and a societal challenge. Liver cancer occurrence in infancy, 1.5 for million children per year, falls far below the threshold of interest for dedicated drug development programs, and this disease is so rare that it is very difficult to gather enough children into a phase II clinical trial. Here, we present the establishment of an unprecedented preclinical platform of 24 pediatric liver cancer patient-derived xenografts (PLC-PDXs) from 20 hepatoblastomas (HBs), 1 transitional liver cell tumor (TCLT), 1 hepatocellular carcinoma, and 2 malignant rhabdoid tumors. Cytogenetic array and mutational analysis of the parental tumors and the corresponding PLC-PDXs show high conservation of the molecular features of the parental tumors. The histology of PLC-PDXs is strikingly similar to that observed in primary tumors and recapitulates the heterogeneity of recurrent disease observed in the clinic. Tumor growth in the mouse is strongly associated with elevated circulating alpha-fetoprotein (AFP), low rate of necrosis/fibrosis after treatment, and gain of chromosome 20, all indicators of resistance to chemotherapy and poor outcome. Accordingly, the ability of a tumor to generate PLC-PDX is predictive of poor prognosis. Exposure of PLC-PDXs to standards of care or therapeutic options already in use for other pediatric malignancies revealed unique response profiles in these models. Among these, the irinotecan/temozolomide combination induced strong tumor regression in the TCLT and in a model derived from an AFP-negative relapsing HB. CONCLUSION These results provide evidence that PLC-PDX preclinical platform can strongly contribute to accelerate the identification and diversification of anticancer treatment for aggressive subtypes of pediatric liver cancer. (Hepatology 2016;64:1121-1135).
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Affiliation(s)
| | - Monique Fabre
- Anathomic Pathology Department, Hôpital Necker Enfants Malades, Paris, France
| | - Marina Simon-Coma
- Childhood Liver Oncology group (c-LOG), Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | | | - Roland Kappler
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Lara Nonell
- Microarray Analysis Facility, Institut Hospital del Mar Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Mar Mallo
- Affymetrix Microarrays Platform and MDS Group, Josep Carreras Leukaemia Research Institute (IJC), ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
| | - Hazar Haidar
- Pharmacogenetic, Molecular Biochemistry and Hormonology Service, Bicêtre Hospital, Paris Sud University, Le Kremlin Bicêtre, France
| | | | - Charlotte Mussini
- Anatomic pathology and Cytopathology Department, Bicêtre Hospital, Paris Sud University, Le Kremlin Bicêtre, France
| | - Catherine Guettier
- Anatomic pathology and Cytopathology Department, Bicêtre Hospital, Paris Sud University, Le Kremlin Bicêtre, France
| | - Marie-José Redon
- Anatomic pathology and Cytopathology Department, Bicêtre Hospital, Paris Sud University, Le Kremlin Bicêtre, France
| | - Laurence Brugières
- Department of Childhood and Adolescence Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Maria Rosa Ghigna
- Department of Pathology, Marie Lannelongue Hospital, Le Plessis Robinson, France
| | - Elie Fadel
- Department of Thoracic and Vascular Surgery, Hôpital Marie Lannelongue, Le Plessis Robinson, France
| | | | - Christophe Chardot
- Department of Pediatric Surgery, Hôpital Necker Enfants Malades, Paris, France
| | | | - Carolina Armengol
- Childhood Liver Oncology group (c-LOG), Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Sophie Branchereau
- Department of Pediatric Surgery, Bicêtre Hospital, Paris Sud University, Le Kremlin Bicêtre, France
| | - Stefano Cairo
- XenTech, 4 rue Pierre Fontaine, Evry, France. .,LTTA Center, Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Italy.
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35
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Nomdedéu JF, Puigdecanet E, Bussaglia E, Hernández JJ, Carricondo M, Estivill C, Martí-Tutusaus JM, Tormo M, Zamora L, Serrano E, Perea G, de Llano MPQ, García A, Sánchez-Ortega I, Ribera JM, Nonell L, Aventin A, Solé F, Brunet MS, Sierra J. Feasibility of the AML profiler (Skyline™ Array) for patient risk stratification in a multicentre trial: a preliminary comparison with the conventional approach. Hematol Oncol 2016; 35:778-788. [PMID: 27140599 DOI: 10.1002/hon.2304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 03/15/2016] [Accepted: 03/31/2016] [Indexed: 12/11/2022]
Abstract
Deoxyribonucleic acid microarrays allow researchers to measure mRNA levels of thousands of genes in a single experiment and could be useful for diagnostic purposes in patients with acute myeloid leukaemia (AML). We assessed the feasibility of the AML profiler (Skyline™ Array) in genetic stratification of patients with de novo AML and compared the results with those obtained using the standard cytogenetic and molecular approach. Diagnostic bone marrow from 31 consecutive de novo AML cases was used to test MLL-PTD, FLT3-ITD and TKD, NPM1 and CEBPAdm mutations. Purified RNA was used to assess RUNX1-RUNX1T1, PML-RARα and CBFβ-MYH11 rearrangements. RNA remnants underwent gene expression profiling analysis using the AML profiler, which detects chromosomal aberrations: t(8;21), t(15;17), inv(16), mutations (CEBPAdm, ABD-NPM1) and BAALC and EVI1 expression. Thirty cases were successfully analysed with both methods. Five cases had FLT3-ITD. In one case, a t(8;21) was correctly detected by both methods. Four cases had inv(16); in one, the RNA quality was unsatisfactory and it was not hybridized, and in the other three, the AML profiler detected the genetic lesion - this being a rare type I translocation in one case. Two cases with acute promyelocytic leukaemia were diagnosed by both methods. Results for NPM1 mutations were concordant in all but two cases (2/11, non-ABD mutations). Analysis of costs and turnaround times showed that the AML profiler was no more expensive than the conventional molecular approach. These results suggest that the AML profiler could be useful in multicentre trials to rapidly identify patients with AML with a good prognosis. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Josep F Nomdedéu
- Hematology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Eulalia Puigdecanet
- Servei d'Analisi de Microarrays, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Elena Bussaglia
- Hematology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | | | - Maite Carricondo
- Hematology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Camino Estivill
- Hematology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | | | - Mar Tormo
- Hematology Department, Hospital Clínico de Valencia, INCLIVA, Valencia, Spain
| | - Lurdes Zamora
- Hematology Department, Institut Recerca contra la Leucemia Josep Carreras (IJC), ICO Badalona Hospital Germans Trias i Pujol, Badalona, Spain
| | - Elena Serrano
- Bioinformatic Platform, IIB Sant Pau, Barcelona, Spain
| | - Granada Perea
- Laboraotory Service, UDIAT-CD, Parc Taulí Hospital Universitari, Sabadell, Spain
| | | | - Antoni García
- Hematology Department, Hospital Arnau de Vilanova, Lleida, Spain
| | | | - Josep Maria Ribera
- Hematology Department, Institut Recerca contra la Leucemia Josep Carreras (IJC), ICO Badalona Hospital Germans Trias i Pujol, Badalona, Spain
| | - Lara Nonell
- Servei d'Analisi de Microarrays, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Anna Aventin
- Hematology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Francesc Solé
- Hematology Department, Institut Recerca contra la Leucemia Josep Carreras (IJC), ICO Badalona Hospital Germans Trias i Pujol, Badalona, Spain
| | - Maria Salut Brunet
- Hematology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Jorge Sierra
- Hematology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
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36
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Ortega FJ, Mercader JM, Moreno-Navarrete JM, Nonell L, Puigdecanet E, Rodriquez-Hermosa JI, Rovira O, Xifra G, Guerra E, Moreno M, Mayas D, Moreno-Castellanos N, Fernández-Formoso JA, Ricart W, Tinahones FJ, Torrents D, Malagón MM, Fernández-Real JM. Surgery-Induced Weight Loss Is Associated With the Downregulation of Genes Targeted by MicroRNAs in Adipose Tissue. J Clin Endocrinol Metab 2015; 100:E1467-76. [PMID: 26252355 DOI: 10.1210/jc.2015-2357] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CONTEXT Molecular mechanisms associated with physiological variations in adipose tissue (AT) are not fully recognized. The most recent reports highlight the critical relevance of microRNAs (miRNAs) found in AT. OBJECTIVE To identify changes in messenger RNA (mRNA) and miRNA expressions and their interaction in human AT before and after surgery-induced weight loss. Research Design and Setting: Genome-wide mRNA and miRNA expressions were assessed by microarrays in abdominal subcutaneous AT of 16 morbidly obese women before and 2 years after laparoscopic Roux-en-Y gastric bypass. The association of changes in miRNAs with their respective mRNA targets was studied. The results were replicated in publicly available microarray datasets. Validation was made by real-time polymerase chain reaction in additional fat samples from 26 age-matched lean women and in isolated human adipocytes. RESULTS A total of 5018 different mRNA probe sets and 15 miRNAs were differentially expressed after surgery-induced weight loss. The clustering of similar expression patterns for gene products with related functions revealed molecular footprints that elucidate significant changes in cell cycle, development, lipid metabolism, and the inflammatory response. The participation of inflammation was demonstrated by results assessed in isolated adipocytes. Interestingly, when transcriptomes were analyzed taking into account the presence of miRNA target sites, miRNA target mRNAs were upregulated in obese AT (P value = 2 × 10(-181)) and inflamed adipocytes (P value = 4 × 10(-61)), according to the number of target sites harbored by each transcript. CONCLUSIONS Current findings suggest impaired miRNA target gene expression in obese AT in close association with inflammation, both improving after weight loss.
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MESH Headings
- Adipocytes, White/cytology
- Adipocytes, White/immunology
- Adipocytes, White/metabolism
- Adult
- Body Mass Index
- Cell Line
- Cells, Cultured
- Cohort Studies
- Cross-Sectional Studies
- Down-Regulation
- Female
- Gastric Bypass
- Gene Expression Profiling
- Genome-Wide Association Study
- Humans
- Longitudinal Studies
- MicroRNAs/metabolism
- Middle Aged
- Monocytes/immunology
- Monocytes/metabolism
- Obesity, Morbid/genetics
- Obesity, Morbid/immunology
- Obesity, Morbid/metabolism
- Obesity, Morbid/surgery
- RNA, Messenger/metabolism
- Subcutaneous Fat, Abdominal/immunology
- Subcutaneous Fat, Abdominal/metabolism
- Weight Loss
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Affiliation(s)
- Francisco J Ortega
- Department of Diabetes, Endocrinology and Nutrition (F.J.O., J.M.M.-N., O.R., G.X., E.G., M.M., W.R., J.M.R.-R.), Institut d'Investigació Biomédica de Girona, Girona, Spain; CIBER de la Fisiopatología de la Obesidad y la Nutrición and Instituto de Salud Carlos III (F.J.O., J.M.M.-N., O.R., D.M., N.M.-C., J.A.F.-F., W.R., F.J.T., M.M.M., J.M.F.-R.), Spain; Joint BSC-CRG-IRB Program on Computational Biology (J.M.M., D.T.), Barcelona Supercomputing Center, Barcelona, Spain; Servei d'Anàlisi de Microarrays (L.N., E.P.), Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain; Department of Surgery (J.I.R.-H.), Institut d'Investigació Biomédica de Girona, Girona, Spain; Service of Endocrinology and Nutrition (D.M., F.J.T.), Hospital Clínico Universitario Virgen de Victoria de Malaga, Málaga, Spain; Department of Cell Biology, Physiology and Immunology (N.M.-C., M.M.M.), Instituto Maimonides de Investigaciones Biomedicas de Cordoba/Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; and Institució Catalana de Recerca i Estudis Avançats (D.T.), Barcelona, Spain
| | - Josep M Mercader
- Department of Diabetes, Endocrinology and Nutrition (F.J.O., J.M.M.-N., O.R., G.X., E.G., M.M., W.R., J.M.R.-R.), Institut d'Investigació Biomédica de Girona, Girona, Spain; CIBER de la Fisiopatología de la Obesidad y la Nutrición and Instituto de Salud Carlos III (F.J.O., J.M.M.-N., O.R., D.M., N.M.-C., J.A.F.-F., W.R., F.J.T., M.M.M., J.M.F.-R.), Spain; Joint BSC-CRG-IRB Program on Computational Biology (J.M.M., D.T.), Barcelona Supercomputing Center, Barcelona, Spain; Servei d'Anàlisi de Microarrays (L.N., E.P.), Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain; Department of Surgery (J.I.R.-H.), Institut d'Investigació Biomédica de Girona, Girona, Spain; Service of Endocrinology and Nutrition (D.M., F.J.T.), Hospital Clínico Universitario Virgen de Victoria de Malaga, Málaga, Spain; Department of Cell Biology, Physiology and Immunology (N.M.-C., M.M.M.), Instituto Maimonides de Investigaciones Biomedicas de Cordoba/Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; and Institució Catalana de Recerca i Estudis Avançats (D.T.), Barcelona, Spain
| | - José M Moreno-Navarrete
- Department of Diabetes, Endocrinology and Nutrition (F.J.O., J.M.M.-N., O.R., G.X., E.G., M.M., W.R., J.M.R.-R.), Institut d'Investigació Biomédica de Girona, Girona, Spain; CIBER de la Fisiopatología de la Obesidad y la Nutrición and Instituto de Salud Carlos III (F.J.O., J.M.M.-N., O.R., D.M., N.M.-C., J.A.F.-F., W.R., F.J.T., M.M.M., J.M.F.-R.), Spain; Joint BSC-CRG-IRB Program on Computational Biology (J.M.M., D.T.), Barcelona Supercomputing Center, Barcelona, Spain; Servei d'Anàlisi de Microarrays (L.N., E.P.), Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain; Department of Surgery (J.I.R.-H.), Institut d'Investigació Biomédica de Girona, Girona, Spain; Service of Endocrinology and Nutrition (D.M., F.J.T.), Hospital Clínico Universitario Virgen de Victoria de Malaga, Málaga, Spain; Department of Cell Biology, Physiology and Immunology (N.M.-C., M.M.M.), Instituto Maimonides de Investigaciones Biomedicas de Cordoba/Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; and Institució Catalana de Recerca i Estudis Avançats (D.T.), Barcelona, Spain
| | - Lara Nonell
- Department of Diabetes, Endocrinology and Nutrition (F.J.O., J.M.M.-N., O.R., G.X., E.G., M.M., W.R., J.M.R.-R.), Institut d'Investigació Biomédica de Girona, Girona, Spain; CIBER de la Fisiopatología de la Obesidad y la Nutrición and Instituto de Salud Carlos III (F.J.O., J.M.M.-N., O.R., D.M., N.M.-C., J.A.F.-F., W.R., F.J.T., M.M.M., J.M.F.-R.), Spain; Joint BSC-CRG-IRB Program on Computational Biology (J.M.M., D.T.), Barcelona Supercomputing Center, Barcelona, Spain; Servei d'Anàlisi de Microarrays (L.N., E.P.), Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain; Department of Surgery (J.I.R.-H.), Institut d'Investigació Biomédica de Girona, Girona, Spain; Service of Endocrinology and Nutrition (D.M., F.J.T.), Hospital Clínico Universitario Virgen de Victoria de Malaga, Málaga, Spain; Department of Cell Biology, Physiology and Immunology (N.M.-C., M.M.M.), Instituto Maimonides de Investigaciones Biomedicas de Cordoba/Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; and Institució Catalana de Recerca i Estudis Avançats (D.T.), Barcelona, Spain
| | - Eulàlia Puigdecanet
- Department of Diabetes, Endocrinology and Nutrition (F.J.O., J.M.M.-N., O.R., G.X., E.G., M.M., W.R., J.M.R.-R.), Institut d'Investigació Biomédica de Girona, Girona, Spain; CIBER de la Fisiopatología de la Obesidad y la Nutrición and Instituto de Salud Carlos III (F.J.O., J.M.M.-N., O.R., D.M., N.M.-C., J.A.F.-F., W.R., F.J.T., M.M.M., J.M.F.-R.), Spain; Joint BSC-CRG-IRB Program on Computational Biology (J.M.M., D.T.), Barcelona Supercomputing Center, Barcelona, Spain; Servei d'Anàlisi de Microarrays (L.N., E.P.), Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain; Department of Surgery (J.I.R.-H.), Institut d'Investigació Biomédica de Girona, Girona, Spain; Service of Endocrinology and Nutrition (D.M., F.J.T.), Hospital Clínico Universitario Virgen de Victoria de Malaga, Málaga, Spain; Department of Cell Biology, Physiology and Immunology (N.M.-C., M.M.M.), Instituto Maimonides de Investigaciones Biomedicas de Cordoba/Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; and Institució Catalana de Recerca i Estudis Avançats (D.T.), Barcelona, Spain
| | - José I Rodriquez-Hermosa
- Department of Diabetes, Endocrinology and Nutrition (F.J.O., J.M.M.-N., O.R., G.X., E.G., M.M., W.R., J.M.R.-R.), Institut d'Investigació Biomédica de Girona, Girona, Spain; CIBER de la Fisiopatología de la Obesidad y la Nutrición and Instituto de Salud Carlos III (F.J.O., J.M.M.-N., O.R., D.M., N.M.-C., J.A.F.-F., W.R., F.J.T., M.M.M., J.M.F.-R.), Spain; Joint BSC-CRG-IRB Program on Computational Biology (J.M.M., D.T.), Barcelona Supercomputing Center, Barcelona, Spain; Servei d'Anàlisi de Microarrays (L.N., E.P.), Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain; Department of Surgery (J.I.R.-H.), Institut d'Investigació Biomédica de Girona, Girona, Spain; Service of Endocrinology and Nutrition (D.M., F.J.T.), Hospital Clínico Universitario Virgen de Victoria de Malaga, Málaga, Spain; Department of Cell Biology, Physiology and Immunology (N.M.-C., M.M.M.), Instituto Maimonides de Investigaciones Biomedicas de Cordoba/Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; and Institució Catalana de Recerca i Estudis Avançats (D.T.), Barcelona, Spain
| | - Oscar Rovira
- Department of Diabetes, Endocrinology and Nutrition (F.J.O., J.M.M.-N., O.R., G.X., E.G., M.M., W.R., J.M.R.-R.), Institut d'Investigació Biomédica de Girona, Girona, Spain; CIBER de la Fisiopatología de la Obesidad y la Nutrición and Instituto de Salud Carlos III (F.J.O., J.M.M.-N., O.R., D.M., N.M.-C., J.A.F.-F., W.R., F.J.T., M.M.M., J.M.F.-R.), Spain; Joint BSC-CRG-IRB Program on Computational Biology (J.M.M., D.T.), Barcelona Supercomputing Center, Barcelona, Spain; Servei d'Anàlisi de Microarrays (L.N., E.P.), Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain; Department of Surgery (J.I.R.-H.), Institut d'Investigació Biomédica de Girona, Girona, Spain; Service of Endocrinology and Nutrition (D.M., F.J.T.), Hospital Clínico Universitario Virgen de Victoria de Malaga, Málaga, Spain; Department of Cell Biology, Physiology and Immunology (N.M.-C., M.M.M.), Instituto Maimonides de Investigaciones Biomedicas de Cordoba/Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; and Institució Catalana de Recerca i Estudis Avançats (D.T.), Barcelona, Spain
| | - Gemma Xifra
- Department of Diabetes, Endocrinology and Nutrition (F.J.O., J.M.M.-N., O.R., G.X., E.G., M.M., W.R., J.M.R.-R.), Institut d'Investigació Biomédica de Girona, Girona, Spain; CIBER de la Fisiopatología de la Obesidad y la Nutrición and Instituto de Salud Carlos III (F.J.O., J.M.M.-N., O.R., D.M., N.M.-C., J.A.F.-F., W.R., F.J.T., M.M.M., J.M.F.-R.), Spain; Joint BSC-CRG-IRB Program on Computational Biology (J.M.M., D.T.), Barcelona Supercomputing Center, Barcelona, Spain; Servei d'Anàlisi de Microarrays (L.N., E.P.), Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain; Department of Surgery (J.I.R.-H.), Institut d'Investigació Biomédica de Girona, Girona, Spain; Service of Endocrinology and Nutrition (D.M., F.J.T.), Hospital Clínico Universitario Virgen de Victoria de Malaga, Málaga, Spain; Department of Cell Biology, Physiology and Immunology (N.M.-C., M.M.M.), Instituto Maimonides de Investigaciones Biomedicas de Cordoba/Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; and Institució Catalana de Recerca i Estudis Avançats (D.T.), Barcelona, Spain
| | - Ester Guerra
- Department of Diabetes, Endocrinology and Nutrition (F.J.O., J.M.M.-N., O.R., G.X., E.G., M.M., W.R., J.M.R.-R.), Institut d'Investigació Biomédica de Girona, Girona, Spain; CIBER de la Fisiopatología de la Obesidad y la Nutrición and Instituto de Salud Carlos III (F.J.O., J.M.M.-N., O.R., D.M., N.M.-C., J.A.F.-F., W.R., F.J.T., M.M.M., J.M.F.-R.), Spain; Joint BSC-CRG-IRB Program on Computational Biology (J.M.M., D.T.), Barcelona Supercomputing Center, Barcelona, Spain; Servei d'Anàlisi de Microarrays (L.N., E.P.), Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain; Department of Surgery (J.I.R.-H.), Institut d'Investigació Biomédica de Girona, Girona, Spain; Service of Endocrinology and Nutrition (D.M., F.J.T.), Hospital Clínico Universitario Virgen de Victoria de Malaga, Málaga, Spain; Department of Cell Biology, Physiology and Immunology (N.M.-C., M.M.M.), Instituto Maimonides de Investigaciones Biomedicas de Cordoba/Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; and Institució Catalana de Recerca i Estudis Avançats (D.T.), Barcelona, Spain
| | - María Moreno
- Department of Diabetes, Endocrinology and Nutrition (F.J.O., J.M.M.-N., O.R., G.X., E.G., M.M., W.R., J.M.R.-R.), Institut d'Investigació Biomédica de Girona, Girona, Spain; CIBER de la Fisiopatología de la Obesidad y la Nutrición and Instituto de Salud Carlos III (F.J.O., J.M.M.-N., O.R., D.M., N.M.-C., J.A.F.-F., W.R., F.J.T., M.M.M., J.M.F.-R.), Spain; Joint BSC-CRG-IRB Program on Computational Biology (J.M.M., D.T.), Barcelona Supercomputing Center, Barcelona, Spain; Servei d'Anàlisi de Microarrays (L.N., E.P.), Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain; Department of Surgery (J.I.R.-H.), Institut d'Investigació Biomédica de Girona, Girona, Spain; Service of Endocrinology and Nutrition (D.M., F.J.T.), Hospital Clínico Universitario Virgen de Victoria de Malaga, Málaga, Spain; Department of Cell Biology, Physiology and Immunology (N.M.-C., M.M.M.), Instituto Maimonides de Investigaciones Biomedicas de Cordoba/Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; and Institució Catalana de Recerca i Estudis Avançats (D.T.), Barcelona, Spain
| | - Dolores Mayas
- Department of Diabetes, Endocrinology and Nutrition (F.J.O., J.M.M.-N., O.R., G.X., E.G., M.M., W.R., J.M.R.-R.), Institut d'Investigació Biomédica de Girona, Girona, Spain; CIBER de la Fisiopatología de la Obesidad y la Nutrición and Instituto de Salud Carlos III (F.J.O., J.M.M.-N., O.R., D.M., N.M.-C., J.A.F.-F., W.R., F.J.T., M.M.M., J.M.F.-R.), Spain; Joint BSC-CRG-IRB Program on Computational Biology (J.M.M., D.T.), Barcelona Supercomputing Center, Barcelona, Spain; Servei d'Anàlisi de Microarrays (L.N., E.P.), Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain; Department of Surgery (J.I.R.-H.), Institut d'Investigació Biomédica de Girona, Girona, Spain; Service of Endocrinology and Nutrition (D.M., F.J.T.), Hospital Clínico Universitario Virgen de Victoria de Malaga, Málaga, Spain; Department of Cell Biology, Physiology and Immunology (N.M.-C., M.M.M.), Instituto Maimonides de Investigaciones Biomedicas de Cordoba/Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; and Institució Catalana de Recerca i Estudis Avançats (D.T.), Barcelona, Spain
| | - Natalia Moreno-Castellanos
- Department of Diabetes, Endocrinology and Nutrition (F.J.O., J.M.M.-N., O.R., G.X., E.G., M.M., W.R., J.M.R.-R.), Institut d'Investigació Biomédica de Girona, Girona, Spain; CIBER de la Fisiopatología de la Obesidad y la Nutrición and Instituto de Salud Carlos III (F.J.O., J.M.M.-N., O.R., D.M., N.M.-C., J.A.F.-F., W.R., F.J.T., M.M.M., J.M.F.-R.), Spain; Joint BSC-CRG-IRB Program on Computational Biology (J.M.M., D.T.), Barcelona Supercomputing Center, Barcelona, Spain; Servei d'Anàlisi de Microarrays (L.N., E.P.), Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain; Department of Surgery (J.I.R.-H.), Institut d'Investigació Biomédica de Girona, Girona, Spain; Service of Endocrinology and Nutrition (D.M., F.J.T.), Hospital Clínico Universitario Virgen de Victoria de Malaga, Málaga, Spain; Department of Cell Biology, Physiology and Immunology (N.M.-C., M.M.M.), Instituto Maimonides de Investigaciones Biomedicas de Cordoba/Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; and Institució Catalana de Recerca i Estudis Avançats (D.T.), Barcelona, Spain
| | - José A Fernández-Formoso
- Department of Diabetes, Endocrinology and Nutrition (F.J.O., J.M.M.-N., O.R., G.X., E.G., M.M., W.R., J.M.R.-R.), Institut d'Investigació Biomédica de Girona, Girona, Spain; CIBER de la Fisiopatología de la Obesidad y la Nutrición and Instituto de Salud Carlos III (F.J.O., J.M.M.-N., O.R., D.M., N.M.-C., J.A.F.-F., W.R., F.J.T., M.M.M., J.M.F.-R.), Spain; Joint BSC-CRG-IRB Program on Computational Biology (J.M.M., D.T.), Barcelona Supercomputing Center, Barcelona, Spain; Servei d'Anàlisi de Microarrays (L.N., E.P.), Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain; Department of Surgery (J.I.R.-H.), Institut d'Investigació Biomédica de Girona, Girona, Spain; Service of Endocrinology and Nutrition (D.M., F.J.T.), Hospital Clínico Universitario Virgen de Victoria de Malaga, Málaga, Spain; Department of Cell Biology, Physiology and Immunology (N.M.-C., M.M.M.), Instituto Maimonides de Investigaciones Biomedicas de Cordoba/Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; and Institució Catalana de Recerca i Estudis Avançats (D.T.), Barcelona, Spain
| | - Wifredo Ricart
- Department of Diabetes, Endocrinology and Nutrition (F.J.O., J.M.M.-N., O.R., G.X., E.G., M.M., W.R., J.M.R.-R.), Institut d'Investigació Biomédica de Girona, Girona, Spain; CIBER de la Fisiopatología de la Obesidad y la Nutrición and Instituto de Salud Carlos III (F.J.O., J.M.M.-N., O.R., D.M., N.M.-C., J.A.F.-F., W.R., F.J.T., M.M.M., J.M.F.-R.), Spain; Joint BSC-CRG-IRB Program on Computational Biology (J.M.M., D.T.), Barcelona Supercomputing Center, Barcelona, Spain; Servei d'Anàlisi de Microarrays (L.N., E.P.), Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain; Department of Surgery (J.I.R.-H.), Institut d'Investigació Biomédica de Girona, Girona, Spain; Service of Endocrinology and Nutrition (D.M., F.J.T.), Hospital Clínico Universitario Virgen de Victoria de Malaga, Málaga, Spain; Department of Cell Biology, Physiology and Immunology (N.M.-C., M.M.M.), Instituto Maimonides de Investigaciones Biomedicas de Cordoba/Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; and Institució Catalana de Recerca i Estudis Avançats (D.T.), Barcelona, Spain
| | - Francisco J Tinahones
- Department of Diabetes, Endocrinology and Nutrition (F.J.O., J.M.M.-N., O.R., G.X., E.G., M.M., W.R., J.M.R.-R.), Institut d'Investigació Biomédica de Girona, Girona, Spain; CIBER de la Fisiopatología de la Obesidad y la Nutrición and Instituto de Salud Carlos III (F.J.O., J.M.M.-N., O.R., D.M., N.M.-C., J.A.F.-F., W.R., F.J.T., M.M.M., J.M.F.-R.), Spain; Joint BSC-CRG-IRB Program on Computational Biology (J.M.M., D.T.), Barcelona Supercomputing Center, Barcelona, Spain; Servei d'Anàlisi de Microarrays (L.N., E.P.), Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain; Department of Surgery (J.I.R.-H.), Institut d'Investigació Biomédica de Girona, Girona, Spain; Service of Endocrinology and Nutrition (D.M., F.J.T.), Hospital Clínico Universitario Virgen de Victoria de Malaga, Málaga, Spain; Department of Cell Biology, Physiology and Immunology (N.M.-C., M.M.M.), Instituto Maimonides de Investigaciones Biomedicas de Cordoba/Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; and Institució Catalana de Recerca i Estudis Avançats (D.T.), Barcelona, Spain
| | - David Torrents
- Department of Diabetes, Endocrinology and Nutrition (F.J.O., J.M.M.-N., O.R., G.X., E.G., M.M., W.R., J.M.R.-R.), Institut d'Investigació Biomédica de Girona, Girona, Spain; CIBER de la Fisiopatología de la Obesidad y la Nutrición and Instituto de Salud Carlos III (F.J.O., J.M.M.-N., O.R., D.M., N.M.-C., J.A.F.-F., W.R., F.J.T., M.M.M., J.M.F.-R.), Spain; Joint BSC-CRG-IRB Program on Computational Biology (J.M.M., D.T.), Barcelona Supercomputing Center, Barcelona, Spain; Servei d'Anàlisi de Microarrays (L.N., E.P.), Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain; Department of Surgery (J.I.R.-H.), Institut d'Investigació Biomédica de Girona, Girona, Spain; Service of Endocrinology and Nutrition (D.M., F.J.T.), Hospital Clínico Universitario Virgen de Victoria de Malaga, Málaga, Spain; Department of Cell Biology, Physiology and Immunology (N.M.-C., M.M.M.), Instituto Maimonides de Investigaciones Biomedicas de Cordoba/Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; and Institució Catalana de Recerca i Estudis Avançats (D.T.), Barcelona, Spain
| | - María M Malagón
- Department of Diabetes, Endocrinology and Nutrition (F.J.O., J.M.M.-N., O.R., G.X., E.G., M.M., W.R., J.M.R.-R.), Institut d'Investigació Biomédica de Girona, Girona, Spain; CIBER de la Fisiopatología de la Obesidad y la Nutrición and Instituto de Salud Carlos III (F.J.O., J.M.M.-N., O.R., D.M., N.M.-C., J.A.F.-F., W.R., F.J.T., M.M.M., J.M.F.-R.), Spain; Joint BSC-CRG-IRB Program on Computational Biology (J.M.M., D.T.), Barcelona Supercomputing Center, Barcelona, Spain; Servei d'Anàlisi de Microarrays (L.N., E.P.), Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain; Department of Surgery (J.I.R.-H.), Institut d'Investigació Biomédica de Girona, Girona, Spain; Service of Endocrinology and Nutrition (D.M., F.J.T.), Hospital Clínico Universitario Virgen de Victoria de Malaga, Málaga, Spain; Department of Cell Biology, Physiology and Immunology (N.M.-C., M.M.M.), Instituto Maimonides de Investigaciones Biomedicas de Cordoba/Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; and Institució Catalana de Recerca i Estudis Avançats (D.T.), Barcelona, Spain
| | - José M Fernández-Real
- Department of Diabetes, Endocrinology and Nutrition (F.J.O., J.M.M.-N., O.R., G.X., E.G., M.M., W.R., J.M.R.-R.), Institut d'Investigació Biomédica de Girona, Girona, Spain; CIBER de la Fisiopatología de la Obesidad y la Nutrición and Instituto de Salud Carlos III (F.J.O., J.M.M.-N., O.R., D.M., N.M.-C., J.A.F.-F., W.R., F.J.T., M.M.M., J.M.F.-R.), Spain; Joint BSC-CRG-IRB Program on Computational Biology (J.M.M., D.T.), Barcelona Supercomputing Center, Barcelona, Spain; Servei d'Anàlisi de Microarrays (L.N., E.P.), Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain; Department of Surgery (J.I.R.-H.), Institut d'Investigació Biomédica de Girona, Girona, Spain; Service of Endocrinology and Nutrition (D.M., F.J.T.), Hospital Clínico Universitario Virgen de Victoria de Malaga, Málaga, Spain; Department of Cell Biology, Physiology and Immunology (N.M.-C., M.M.M.), Instituto Maimonides de Investigaciones Biomedicas de Cordoba/Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; and Institució Catalana de Recerca i Estudis Avançats (D.T.), Barcelona, Spain
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Pavlovic M, Arnal-Estapé A, Rojo F, Bellmunt A, Tarragona M, Guiu M, Planet E, Garcia-Albéniz X, Morales M, Urosevic J, Gawrzak S, Rovira A, Prat A, Nonell L, Lluch A, Jean-Mairet J, Coleman R, Albanell J, Gomis RR. Enhanced MAF Oncogene Expression and Breast Cancer Bone Metastasis. J Natl Cancer Inst 2015; 107:djv256. [PMID: 26376684 PMCID: PMC4681582 DOI: 10.1093/jnci/djv256] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 08/18/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND There are currently no biomarkers for early breast cancer patient populations at risk of bone metastasis. Identification of mediators of bone metastasis could be of clinical interest. METHODS A de novo unbiased screening approach based on selection of highly bone metastatic breast cancer cells in vivo was used to determine copy number aberrations (CNAs) associated with bone metastasis. The CNAs associated with bone metastasis were examined in independent primary breast cancer datasets with annotated clinical follow-up. The MAF gene encoded within the CNA associated with bone metastasis was subjected to gain and loss of function validation in breast cancer cells (MCF7, T47D, ZR-75, and 4T1), its downstream mechanism validated, and tested in clinical samples. A multivariable Cox cause-specific hazard model with competing events (death) was used to test the association between 16q23 or MAF and bone metastasis. All statistical tests were two-sided. RESULTS 16q23 gain CNA encoding the transcription factor MAF mediates breast cancer bone metastasis through the control of PTHrP. 16q23 gain (hazard ratio (HR) for bone metastasis = 14.5, 95% confidence interval (CI) = 6.4 to 32.9, P < .001) as well as MAF overexpression (HR for bone metastasis = 2.5, 95% CI = 1.7 to 3.8, P < .001) in primary breast tumors were specifically associated with risk of metastasis to bone but not to other organs. CONCLUSIONS These results suggest that MAF is a mediator of breast cancer bone metastasis. 16q23 gain or MAF protein overexpression in tumors may help to select patients at risk of bone relapse.
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Affiliation(s)
- Milica Pavlovic
- Oncology Program (MP, AAE, AB, MT, MG, XGA, MM, JU, SG, RRG) and Biostatistics and Bioinformatics Unit (EP), Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Cancer Research Program (FR, AR, JA) and Microarray Analysis Service (LN), IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, IIS-Fundación Jimenez Diaz, Madrid, Spain (FR); Medical Oncology Service, Hospital del Mar, Barcelona, Spain (AR, JA); Department of Oncology and Hematology, Hospital Clínico Universitario, Valencia, Spain (AL); Valencia Central University, Spain (AL); Inbiomotion, Barcelona, Spain (JJM); Sheffield Cancer Research Centre, Sheffield, UK (RC); Universitat Pompeu Fabra, Barcelona, Spain (JA); Translational Genomics, Vall d'Hebron Insitute of Oncology, Barcelona, Spain (AP); Department of Epidemiology, Harvard School of Public Health, Boston, MA (XGA); Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain (RRG)
| | - Anna Arnal-Estapé
- Oncology Program (MP, AAE, AB, MT, MG, XGA, MM, JU, SG, RRG) and Biostatistics and Bioinformatics Unit (EP), Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Cancer Research Program (FR, AR, JA) and Microarray Analysis Service (LN), IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, IIS-Fundación Jimenez Diaz, Madrid, Spain (FR); Medical Oncology Service, Hospital del Mar, Barcelona, Spain (AR, JA); Department of Oncology and Hematology, Hospital Clínico Universitario, Valencia, Spain (AL); Valencia Central University, Spain (AL); Inbiomotion, Barcelona, Spain (JJM); Sheffield Cancer Research Centre, Sheffield, UK (RC); Universitat Pompeu Fabra, Barcelona, Spain (JA); Translational Genomics, Vall d'Hebron Insitute of Oncology, Barcelona, Spain (AP); Department of Epidemiology, Harvard School of Public Health, Boston, MA (XGA); Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain (RRG)
| | - Federico Rojo
- Oncology Program (MP, AAE, AB, MT, MG, XGA, MM, JU, SG, RRG) and Biostatistics and Bioinformatics Unit (EP), Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Cancer Research Program (FR, AR, JA) and Microarray Analysis Service (LN), IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, IIS-Fundación Jimenez Diaz, Madrid, Spain (FR); Medical Oncology Service, Hospital del Mar, Barcelona, Spain (AR, JA); Department of Oncology and Hematology, Hospital Clínico Universitario, Valencia, Spain (AL); Valencia Central University, Spain (AL); Inbiomotion, Barcelona, Spain (JJM); Sheffield Cancer Research Centre, Sheffield, UK (RC); Universitat Pompeu Fabra, Barcelona, Spain (JA); Translational Genomics, Vall d'Hebron Insitute of Oncology, Barcelona, Spain (AP); Department of Epidemiology, Harvard School of Public Health, Boston, MA (XGA); Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain (RRG)
| | - Anna Bellmunt
- Oncology Program (MP, AAE, AB, MT, MG, XGA, MM, JU, SG, RRG) and Biostatistics and Bioinformatics Unit (EP), Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Cancer Research Program (FR, AR, JA) and Microarray Analysis Service (LN), IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, IIS-Fundación Jimenez Diaz, Madrid, Spain (FR); Medical Oncology Service, Hospital del Mar, Barcelona, Spain (AR, JA); Department of Oncology and Hematology, Hospital Clínico Universitario, Valencia, Spain (AL); Valencia Central University, Spain (AL); Inbiomotion, Barcelona, Spain (JJM); Sheffield Cancer Research Centre, Sheffield, UK (RC); Universitat Pompeu Fabra, Barcelona, Spain (JA); Translational Genomics, Vall d'Hebron Insitute of Oncology, Barcelona, Spain (AP); Department of Epidemiology, Harvard School of Public Health, Boston, MA (XGA); Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain (RRG)
| | - Maria Tarragona
- Oncology Program (MP, AAE, AB, MT, MG, XGA, MM, JU, SG, RRG) and Biostatistics and Bioinformatics Unit (EP), Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Cancer Research Program (FR, AR, JA) and Microarray Analysis Service (LN), IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, IIS-Fundación Jimenez Diaz, Madrid, Spain (FR); Medical Oncology Service, Hospital del Mar, Barcelona, Spain (AR, JA); Department of Oncology and Hematology, Hospital Clínico Universitario, Valencia, Spain (AL); Valencia Central University, Spain (AL); Inbiomotion, Barcelona, Spain (JJM); Sheffield Cancer Research Centre, Sheffield, UK (RC); Universitat Pompeu Fabra, Barcelona, Spain (JA); Translational Genomics, Vall d'Hebron Insitute of Oncology, Barcelona, Spain (AP); Department of Epidemiology, Harvard School of Public Health, Boston, MA (XGA); Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain (RRG)
| | - Marc Guiu
- Oncology Program (MP, AAE, AB, MT, MG, XGA, MM, JU, SG, RRG) and Biostatistics and Bioinformatics Unit (EP), Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Cancer Research Program (FR, AR, JA) and Microarray Analysis Service (LN), IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, IIS-Fundación Jimenez Diaz, Madrid, Spain (FR); Medical Oncology Service, Hospital del Mar, Barcelona, Spain (AR, JA); Department of Oncology and Hematology, Hospital Clínico Universitario, Valencia, Spain (AL); Valencia Central University, Spain (AL); Inbiomotion, Barcelona, Spain (JJM); Sheffield Cancer Research Centre, Sheffield, UK (RC); Universitat Pompeu Fabra, Barcelona, Spain (JA); Translational Genomics, Vall d'Hebron Insitute of Oncology, Barcelona, Spain (AP); Department of Epidemiology, Harvard School of Public Health, Boston, MA (XGA); Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain (RRG)
| | - Evarist Planet
- Oncology Program (MP, AAE, AB, MT, MG, XGA, MM, JU, SG, RRG) and Biostatistics and Bioinformatics Unit (EP), Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Cancer Research Program (FR, AR, JA) and Microarray Analysis Service (LN), IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, IIS-Fundación Jimenez Diaz, Madrid, Spain (FR); Medical Oncology Service, Hospital del Mar, Barcelona, Spain (AR, JA); Department of Oncology and Hematology, Hospital Clínico Universitario, Valencia, Spain (AL); Valencia Central University, Spain (AL); Inbiomotion, Barcelona, Spain (JJM); Sheffield Cancer Research Centre, Sheffield, UK (RC); Universitat Pompeu Fabra, Barcelona, Spain (JA); Translational Genomics, Vall d'Hebron Insitute of Oncology, Barcelona, Spain (AP); Department of Epidemiology, Harvard School of Public Health, Boston, MA (XGA); Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain (RRG)
| | - Xabier Garcia-Albéniz
- Oncology Program (MP, AAE, AB, MT, MG, XGA, MM, JU, SG, RRG) and Biostatistics and Bioinformatics Unit (EP), Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Cancer Research Program (FR, AR, JA) and Microarray Analysis Service (LN), IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, IIS-Fundación Jimenez Diaz, Madrid, Spain (FR); Medical Oncology Service, Hospital del Mar, Barcelona, Spain (AR, JA); Department of Oncology and Hematology, Hospital Clínico Universitario, Valencia, Spain (AL); Valencia Central University, Spain (AL); Inbiomotion, Barcelona, Spain (JJM); Sheffield Cancer Research Centre, Sheffield, UK (RC); Universitat Pompeu Fabra, Barcelona, Spain (JA); Translational Genomics, Vall d'Hebron Insitute of Oncology, Barcelona, Spain (AP); Department of Epidemiology, Harvard School of Public Health, Boston, MA (XGA); Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain (RRG)
| | - Mónica Morales
- Oncology Program (MP, AAE, AB, MT, MG, XGA, MM, JU, SG, RRG) and Biostatistics and Bioinformatics Unit (EP), Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Cancer Research Program (FR, AR, JA) and Microarray Analysis Service (LN), IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, IIS-Fundación Jimenez Diaz, Madrid, Spain (FR); Medical Oncology Service, Hospital del Mar, Barcelona, Spain (AR, JA); Department of Oncology and Hematology, Hospital Clínico Universitario, Valencia, Spain (AL); Valencia Central University, Spain (AL); Inbiomotion, Barcelona, Spain (JJM); Sheffield Cancer Research Centre, Sheffield, UK (RC); Universitat Pompeu Fabra, Barcelona, Spain (JA); Translational Genomics, Vall d'Hebron Insitute of Oncology, Barcelona, Spain (AP); Department of Epidemiology, Harvard School of Public Health, Boston, MA (XGA); Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain (RRG)
| | - Jelena Urosevic
- Oncology Program (MP, AAE, AB, MT, MG, XGA, MM, JU, SG, RRG) and Biostatistics and Bioinformatics Unit (EP), Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Cancer Research Program (FR, AR, JA) and Microarray Analysis Service (LN), IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, IIS-Fundación Jimenez Diaz, Madrid, Spain (FR); Medical Oncology Service, Hospital del Mar, Barcelona, Spain (AR, JA); Department of Oncology and Hematology, Hospital Clínico Universitario, Valencia, Spain (AL); Valencia Central University, Spain (AL); Inbiomotion, Barcelona, Spain (JJM); Sheffield Cancer Research Centre, Sheffield, UK (RC); Universitat Pompeu Fabra, Barcelona, Spain (JA); Translational Genomics, Vall d'Hebron Insitute of Oncology, Barcelona, Spain (AP); Department of Epidemiology, Harvard School of Public Health, Boston, MA (XGA); Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain (RRG)
| | - Sylwia Gawrzak
- Oncology Program (MP, AAE, AB, MT, MG, XGA, MM, JU, SG, RRG) and Biostatistics and Bioinformatics Unit (EP), Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Cancer Research Program (FR, AR, JA) and Microarray Analysis Service (LN), IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, IIS-Fundación Jimenez Diaz, Madrid, Spain (FR); Medical Oncology Service, Hospital del Mar, Barcelona, Spain (AR, JA); Department of Oncology and Hematology, Hospital Clínico Universitario, Valencia, Spain (AL); Valencia Central University, Spain (AL); Inbiomotion, Barcelona, Spain (JJM); Sheffield Cancer Research Centre, Sheffield, UK (RC); Universitat Pompeu Fabra, Barcelona, Spain (JA); Translational Genomics, Vall d'Hebron Insitute of Oncology, Barcelona, Spain (AP); Department of Epidemiology, Harvard School of Public Health, Boston, MA (XGA); Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain (RRG)
| | - Ana Rovira
- Oncology Program (MP, AAE, AB, MT, MG, XGA, MM, JU, SG, RRG) and Biostatistics and Bioinformatics Unit (EP), Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Cancer Research Program (FR, AR, JA) and Microarray Analysis Service (LN), IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, IIS-Fundación Jimenez Diaz, Madrid, Spain (FR); Medical Oncology Service, Hospital del Mar, Barcelona, Spain (AR, JA); Department of Oncology and Hematology, Hospital Clínico Universitario, Valencia, Spain (AL); Valencia Central University, Spain (AL); Inbiomotion, Barcelona, Spain (JJM); Sheffield Cancer Research Centre, Sheffield, UK (RC); Universitat Pompeu Fabra, Barcelona, Spain (JA); Translational Genomics, Vall d'Hebron Insitute of Oncology, Barcelona, Spain (AP); Department of Epidemiology, Harvard School of Public Health, Boston, MA (XGA); Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain (RRG)
| | - Aleix Prat
- Oncology Program (MP, AAE, AB, MT, MG, XGA, MM, JU, SG, RRG) and Biostatistics and Bioinformatics Unit (EP), Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Cancer Research Program (FR, AR, JA) and Microarray Analysis Service (LN), IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, IIS-Fundación Jimenez Diaz, Madrid, Spain (FR); Medical Oncology Service, Hospital del Mar, Barcelona, Spain (AR, JA); Department of Oncology and Hematology, Hospital Clínico Universitario, Valencia, Spain (AL); Valencia Central University, Spain (AL); Inbiomotion, Barcelona, Spain (JJM); Sheffield Cancer Research Centre, Sheffield, UK (RC); Universitat Pompeu Fabra, Barcelona, Spain (JA); Translational Genomics, Vall d'Hebron Insitute of Oncology, Barcelona, Spain (AP); Department of Epidemiology, Harvard School of Public Health, Boston, MA (XGA); Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain (RRG)
| | - Lara Nonell
- Oncology Program (MP, AAE, AB, MT, MG, XGA, MM, JU, SG, RRG) and Biostatistics and Bioinformatics Unit (EP), Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Cancer Research Program (FR, AR, JA) and Microarray Analysis Service (LN), IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, IIS-Fundación Jimenez Diaz, Madrid, Spain (FR); Medical Oncology Service, Hospital del Mar, Barcelona, Spain (AR, JA); Department of Oncology and Hematology, Hospital Clínico Universitario, Valencia, Spain (AL); Valencia Central University, Spain (AL); Inbiomotion, Barcelona, Spain (JJM); Sheffield Cancer Research Centre, Sheffield, UK (RC); Universitat Pompeu Fabra, Barcelona, Spain (JA); Translational Genomics, Vall d'Hebron Insitute of Oncology, Barcelona, Spain (AP); Department of Epidemiology, Harvard School of Public Health, Boston, MA (XGA); Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain (RRG)
| | - Ana Lluch
- Oncology Program (MP, AAE, AB, MT, MG, XGA, MM, JU, SG, RRG) and Biostatistics and Bioinformatics Unit (EP), Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Cancer Research Program (FR, AR, JA) and Microarray Analysis Service (LN), IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, IIS-Fundación Jimenez Diaz, Madrid, Spain (FR); Medical Oncology Service, Hospital del Mar, Barcelona, Spain (AR, JA); Department of Oncology and Hematology, Hospital Clínico Universitario, Valencia, Spain (AL); Valencia Central University, Spain (AL); Inbiomotion, Barcelona, Spain (JJM); Sheffield Cancer Research Centre, Sheffield, UK (RC); Universitat Pompeu Fabra, Barcelona, Spain (JA); Translational Genomics, Vall d'Hebron Insitute of Oncology, Barcelona, Spain (AP); Department of Epidemiology, Harvard School of Public Health, Boston, MA (XGA); Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain (RRG)
| | - Joël Jean-Mairet
- Oncology Program (MP, AAE, AB, MT, MG, XGA, MM, JU, SG, RRG) and Biostatistics and Bioinformatics Unit (EP), Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Cancer Research Program (FR, AR, JA) and Microarray Analysis Service (LN), IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, IIS-Fundación Jimenez Diaz, Madrid, Spain (FR); Medical Oncology Service, Hospital del Mar, Barcelona, Spain (AR, JA); Department of Oncology and Hematology, Hospital Clínico Universitario, Valencia, Spain (AL); Valencia Central University, Spain (AL); Inbiomotion, Barcelona, Spain (JJM); Sheffield Cancer Research Centre, Sheffield, UK (RC); Universitat Pompeu Fabra, Barcelona, Spain (JA); Translational Genomics, Vall d'Hebron Insitute of Oncology, Barcelona, Spain (AP); Department of Epidemiology, Harvard School of Public Health, Boston, MA (XGA); Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain (RRG)
| | - Robert Coleman
- Oncology Program (MP, AAE, AB, MT, MG, XGA, MM, JU, SG, RRG) and Biostatistics and Bioinformatics Unit (EP), Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Cancer Research Program (FR, AR, JA) and Microarray Analysis Service (LN), IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, IIS-Fundación Jimenez Diaz, Madrid, Spain (FR); Medical Oncology Service, Hospital del Mar, Barcelona, Spain (AR, JA); Department of Oncology and Hematology, Hospital Clínico Universitario, Valencia, Spain (AL); Valencia Central University, Spain (AL); Inbiomotion, Barcelona, Spain (JJM); Sheffield Cancer Research Centre, Sheffield, UK (RC); Universitat Pompeu Fabra, Barcelona, Spain (JA); Translational Genomics, Vall d'Hebron Insitute of Oncology, Barcelona, Spain (AP); Department of Epidemiology, Harvard School of Public Health, Boston, MA (XGA); Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain (RRG)
| | - Joan Albanell
- Oncology Program (MP, AAE, AB, MT, MG, XGA, MM, JU, SG, RRG) and Biostatistics and Bioinformatics Unit (EP), Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Cancer Research Program (FR, AR, JA) and Microarray Analysis Service (LN), IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, IIS-Fundación Jimenez Diaz, Madrid, Spain (FR); Medical Oncology Service, Hospital del Mar, Barcelona, Spain (AR, JA); Department of Oncology and Hematology, Hospital Clínico Universitario, Valencia, Spain (AL); Valencia Central University, Spain (AL); Inbiomotion, Barcelona, Spain (JJM); Sheffield Cancer Research Centre, Sheffield, UK (RC); Universitat Pompeu Fabra, Barcelona, Spain (JA); Translational Genomics, Vall d'Hebron Insitute of Oncology, Barcelona, Spain (AP); Department of Epidemiology, Harvard School of Public Health, Boston, MA (XGA); Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain (RRG)
| | - Roger R Gomis
- Oncology Program (MP, AAE, AB, MT, MG, XGA, MM, JU, SG, RRG) and Biostatistics and Bioinformatics Unit (EP), Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain; Cancer Research Program (FR, AR, JA) and Microarray Analysis Service (LN), IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Pathology Department, IIS-Fundación Jimenez Diaz, Madrid, Spain (FR); Medical Oncology Service, Hospital del Mar, Barcelona, Spain (AR, JA); Department of Oncology and Hematology, Hospital Clínico Universitario, Valencia, Spain (AL); Valencia Central University, Spain (AL); Inbiomotion, Barcelona, Spain (JJM); Sheffield Cancer Research Centre, Sheffield, UK (RC); Universitat Pompeu Fabra, Barcelona, Spain (JA); Translational Genomics, Vall d'Hebron Insitute of Oncology, Barcelona, Spain (AP); Department of Epidemiology, Harvard School of Public Health, Boston, MA (XGA); Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain (RRG).
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de la Chica RA, de Lara À, Nonell L, Clusellas N. Structural chromosome rearrangements in prenatal diagnosis: results from a Spanish database. Eur J Obstet Gynecol Reprod Biol 2015; 194:252-4. [PMID: 26227736 DOI: 10.1016/j.ejogrb.2015.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 07/07/2015] [Indexed: 10/23/2022]
Affiliation(s)
| | | | - Lara Nonell
- Servei d'Anàlisi de Microarrays, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
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Gallardo F, Padrón A, Garcia-Carbonell R, Rius C, González-Perez A, Arumí-Uria M, Iglesias M, Nonell L, Bellosillo B, Segura S, Pujol RM, Lopez-Bigas N, Bertran J, Bigas A, Espinosa L. Cytoplasmic accumulation of NCoR in malignant melanoma: consequences of altered gene repression and prognostic significance. Oncotarget 2015; 6:9284-94. [PMID: 25823659 PMCID: PMC4496217 DOI: 10.18632/oncotarget.3252] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [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: 11/24/2014] [Accepted: 01/31/2015] [Indexed: 11/25/2022] Open
Abstract
Invasive malignant melanoma (MM) is an aggressive tumor with no curative therapy available in advanced stages. Nuclear corepressor (NCoR) is an essential regulator of gene transcription, and its function has been found deregulated in different types of cancer. In colorectal cancer cells, loss of nuclear NCoR is induced by Inhibitor of kappa B kinase (IKK) through the phosphorylation of specific serine residues. We here investigate whether NCoR function impacts in MM, which might have important diagnostic and prognostic significance. By IHC, we here determined the subcellular distribution of NCoR in a cohort of 63 primary invasive MM samples, and analyzed its possible correlation with specific clinical parameters. We therefore used a microarray-based strategy to determine global gene expression differences in samples with similar tumor stage, which differ in the presence of cytoplasmic or nuclear NCoR. We found that loss of nuclear NCoR results in upregulation of a specific cancer-related genetic signature, and is significantly associated with MM progression. Inhibition of IKK activity in melanoma cells reverts NCoR nuclear distribution and specific NCoR-regulated gene transcription. Analysis of public database demonstrated that inactivating NCoR mutations are highly prevalent in MM, showing features of driver oncogene.
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Affiliation(s)
- Fernando Gallardo
- Dermatology Department, Parc de Salut Mar-Hospital del Mar, Barcelona, Spain
| | - Andreina Padrón
- Pathology Department, Parc de Salut Mar-Hospital del Mar, Barcelona, Spain
| | - Ricard Garcia-Carbonell
- Stem Cells and Cancer Research Laboratory, Institut Hospital del Mar Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Cristina Rius
- Stem Cells and Cancer Research Laboratory, Institut Hospital del Mar Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Abel González-Perez
- Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Mar Iglesias
- Pathology Department, Parc de Salut Mar-Hospital del Mar, Barcelona, Spain
| | - Lara Nonell
- Servei d’Anàlisi de Microarrays, Institut Hospital del Mar Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Beatriz Bellosillo
- Pathology Department, Parc de Salut Mar-Hospital del Mar, Barcelona, Spain
| | - Sonia Segura
- Dermatology Department, Parc de Salut Mar-Hospital del Mar, Barcelona, Spain
| | - Ramon Maria Pujol
- Dermatology Department, Parc de Salut Mar-Hospital del Mar, Barcelona, Spain
| | - Nuria Lopez-Bigas
- Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys, Barcelona, Spain
| | - Joan Bertran
- Universitat de Vic, Universitat Central de Catalunya (UVic-UCC), Vic, Spain
| | - Anna Bigas
- Stem Cells and Cancer Research Laboratory, Institut Hospital del Mar Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Lluís Espinosa
- Stem Cells and Cancer Research Laboratory, Institut Hospital del Mar Investigacions Mèdiques (IMIM), Barcelona, Spain
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Espinet B, Ferrer A, Bellosillo B, Nonell L, Salar A, Fernández-Rodríguez C, Puigdecanet E, Gimeno J, Garcia-Garcia M, Vela MC, Luño E, Collado R, Navarro JT, de la Banda E, Abrisqueta P, Arenillas L, Serrano C, Lloreta J, Miñana B, Cerutti A, Florensa L, Orfao A, Sanz F, Solé F, Dominguez-Sola D, Serrano S. Distinction between asymptomatic monoclonal B-cell lymphocytosis with cyclin D1 overexpression and mantle cell lymphoma: from molecular profiling to flow cytometry. Clin Cancer Res 2013; 20:1007-19. [PMID: 24352646 DOI: 10.1158/1078-0432.ccr-13-1077] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE According to current diagnostic criteria, mantle cell lymphoma (MCL) encompasses the usual, aggressive variants and rare, nonnodal cases with monoclonal asymptomatic lymphocytosis, cyclin D1-positive (MALD1). We aimed to understand the biology behind this clinical heterogeneity and to identify markers for adequate identification of MALD1 cases. EXPERIMENTAL DESIGN We compared 17 typical MCL cases with a homogeneous group of 13 untreated MALD1 cases (median follow-up, 71 months). We conducted gene expression profiling with functional analysis in five MCL and five MALD1. Results were validated in 12 MCL and 8 MALD1 additional cases by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and in 24 MCL and 13 MALD1 cases by flow cytometry. Classification and regression trees strategy was used to generate an algorithm based on CD38 and CD200 expression by flow cytometry. RESULTS We found 171 differentially expressed genes with enrichment of neoplastic behavior and cell proliferation signatures in MCL. Conversely, MALD1 was enriched in gene sets related to immune activation and inflammatory responses. CD38 and CD200 were differentially expressed between MCL and MALD1 and confirmed by flow cytometry (median CD38, 89% vs. 14%; median CD200, 0% vs. 24%, respectively). Assessment of both proteins allowed classifying 85% (11 of 13) of MALD1 cases whereas 15% remained unclassified. SOX11 expression by qRT-PCR was significantly different between MCL and MALD1 groups but did not improve the classification. CONCLUSION We show for the first time that MALD1, in contrast to MCL, is characterized by immune activation and driven by inflammatory cues. Assessment of CD38/CD200 by flow cytometry is useful to distinguish most cases of MALD1 from MCL in the clinical setting. MALD1 should be identified and segregated from the current MCL category to avoid overdiagnosis and unnecessary treatment.
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Affiliation(s)
- Blanca Espinet
- Authors' Affiliations: Servei de Patologia, Servei d'Hematologia, Hospital del Mar; Programa de Recerca en Càncer, Servei d'Anàlisi de Microarrays, Institut Català de Recerca i Estudis Avançats (ICREA), Research Programme on Biomedical Informatics (GRIB), IMIM, Universitat Pompeu Fabra, PRBB; Servei d'Hematología, ICO-Hospital Germans Trias i Pujol; Servei d'Hematologia, IDIBELL-Hospital de Bellvitge, L'Hospitalet de Llobregat; Servei d'Hematologia, Hospital Universitari Vall d'Hebron; Centre de Regulació Genòmica, Barcelona; Servicio de Hematología, Hospital Universitario Central de Asturias, Oviedo; Servicio de Hematología, Hospital General Universitario de Valencia, Valencia; Laboratorio de Citometría de Flujo, Servicio de Hematología, Fundación Jiménez Díaz, Madrid; Servicio General de Citometría, Centro de Investigación del Cáncer (IBMCC-CSIC/USAL and IBSAL) and Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain; Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York; and Universitat Autònoma de Barcelona
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41
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Rojo F, Domingo L, Sala M, Zazo S, Chamizo C, Menendez S, Arpi O, Corominas JM, Bragado R, Servitja S, Tusquets I, Nonell L, Macià F, Martínez J, Rovira A, Albanell J, Castells X. Gene expression profiling in true interval breast cancer reveals overactivation of the mTOR signaling pathway. Cancer Epidemiol Biomarkers Prev 2013; 23:288-99. [PMID: 24347552 DOI: 10.1158/1055-9965.epi-13-0761] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The development and progression of true interval breast cancers (tumors that truly appear after a negative screening mammogram) is known to be different from screen-detected cancers. However, the worse clinical behavior of true interval cancers is not fully understood from a biologic basis. We described the differential patterns of gene expression through microarray analysis in true interval and screen-detected cancers. METHODS An unsupervised exploratory gene expression profile analysis was performed on 10 samples (true interval cancers = 5; screen-detected cancers = 5) using Affymetrix Human Gene 1.0ST arrays and interpreted by Ingenuity Pathway Analysis. Differential expression of selected genes was confirmed in a validation series of 91 tumors (n = 12; n = 79) by immunohistochemistry and in 24 tumors (n = 8; n = 16) by reverse transcription quantitative PCR (RT-qPCR), in true interval and screen-detected cancers, respectively. RESULTS Exploratory gene expression analysis identified 1,060 differentially expressed genes (unadjusted P < 0.05) between study groups. On the basis of biologic implications, four genes were further validated: ceruloplasmin (CP) and ribosomal protein S6 kinase, 70 kDa, polypeptide 2 (RPS6KB2), both upregulated in true interval cancers; and phosphatase and tensin homolog (PTEN) and transforming growth factor beta receptor III (TGFBR3), downregulated in true interval cancers. Their differential expression was confirmed by RT-qPCR and immunohistochemistry, consistent with mTOR pathway overexpression in true interval cancers. CONCLUSIONS True interval and screen-detected cancers show differential expression profile both at gene and protein levels. The mTOR signaling is significantly upregulated in true interval cancers, suggesting this pathway may mediate their aggressiveness. IMPACT Linking epidemiologic factors and mTOR activation may be the basis for future personalized screening strategies in women at risk of true interval cancers.
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Affiliation(s)
- Federico Rojo
- Authors' Affiliations: Departments of Pathology and Immunology, IIS-Fundación Jiménez Díaz, Madrid; Cancer Research Program; Microarray Core Facility (SAM), IMIM (Hospital del Mar Medical Research Institute); Department of Epidemiology and Evaluation, Hospital del Mar; Research Network on Health Services in Chronic Diseases (REDISSEC); Departments of Pathology, Medical Oncology, and Radiology Department, Hospital del Mar; and Universitat Pompeu Fabra, Barcelona, Spain
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42
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Castañer O, Corella D, Covas MI, Sorlí JV, Subirana I, Flores-Mateo G, Nonell L, Bulló M, de la Torre R, Portolés O, Fitó M. In vivo transcriptomic profile after a Mediterranean diet in high-cardiovascular risk patients: a randomized controlled trial. Am J Clin Nutr 2013; 98:845-53. [PMID: 23902780 DOI: 10.3945/ajcn.113.060582] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Nutrients can exert healthy effects through nutrigenomic modulation. Data are scarce concerning the in vivo effect of a sustained traditional Mediterranean diet (TMD) pattern on the whole transcriptomic response. OBJECTIVE We explored the overall nutrigenomic effect associated with a TMD. DESIGN We focused on biological pathways related to cardiovascular disease (CVD) in a subsample (n = 34) of the Prevención Con Dieta Mediterránea (PREDIMED) study, which was a large, parallel-group, multicenter, randomized controlled trial that aimed to assess the effects of TMD on the primary prevention of CVD in individuals with high cardiovascular risk. Participants were randomly assigned to a low-fat diet control group or TMD intervention groups [traditional Mediterranean diet supplemented with virgin olive oil (TMD+VOO) or traditional Mediterranean diet supplemented with nuts (TMD+Nuts)] in equal proportions. Three-month changes in whole genome peripheral blood mononuclear cells were assessed by using whole transcriptome microarray analyses. RESULTS A functional annotation analysis was performed on 241 selected responder genes after the TMD+VOO (139 upregulated and 102 downregulated genes), 312 selected responder genes after the TMD+Nuts (165 upregulated and 147 downregulated genes), and 145 selected responder genes after the low-fat (100 upregulated and 45 downregulated genes) diets. Of 18 cardiovascular canonical pathway analyses, 12 pathways were differentially expressed, and 43% of pathways were modulated by both TMDs; the most prevalent pathways were related to atherosclerosis and hypertension. After simultaneous testing adjustment, 9 pathways were modulated by the TMD+VOO diet, and 4 pathways were modulated by the TMD+Nuts diet. CONCLUSION One of the mechanisms by which TMD, particularly if supplemented with virgin olive oil, can exert health benefits is through changes in the transcriptomic response of genes related to cardiovascular risk. This trial was registered at the London-based Current Controlled Trials register as ISRCTN35739639.
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Affiliation(s)
- Olga Castañer
- Cardiovascular Risk and Nutrition Research Group, Hospital del Mar Research Institute, Barcelona, Spain
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43
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Agell L, Hernández S, Nonell L, Lorenzo M, Puigdecanet E, de Muga S, Juanpere N, Bermudo R, Fernández PL, Lorente JA, Serrano S, Lloreta J. A 12-gene expression signature is associated with aggressive histological in prostate cancer: SEC14L1 and TCEB1 genes are potential markers of progression. Am J Pathol 2013; 181:1585-94. [PMID: 23083832 DOI: 10.1016/j.ajpath.2012.08.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 07/24/2012] [Accepted: 08/01/2012] [Indexed: 01/08/2023]
Abstract
The main challenge for clinical management of prostate cancer is to distinguish tumors that will progress faster and will show a higher tendency to recur from the more indolent ones. We have compared expression profiles of 18 prostate cancer samples (seven with a Gleason score of 6, eight with a Gleason score of 7, and three with a Gleason score of ≥8) and five nonneoplastic prostate samples, using the Affymetrix Human Array GeneChip Exon 1.0 ST. Microarray analysis revealed 99 genes showing statistically significant differences among tumors with Gleason scores of 6, 7, and ≥8. In addition, mRNA expression of 29 selected genes was analyzed by real-time quantitative RT-PCR with microfluidic cards in an extended series of 30 prostate tumors. Of the 29 genes, 18 (62%) were independently confirmed in the extended series by quantitative RT-PCR: 14 were up-regulated and 4 were down-regulated in tumors with a higher Gleason score. Twelve of these genes were differentially expressed in tumors with a Gleason score of 6 to 7 versus ≥8. Finally, IHC validation of the protein levels of two genes from the 12-gene signature (SEC14L1 and TCEB1) showed strong protein expression levels of both genes, which were statistically associated with a high combined Gleason score, advanced stage, and prostate-specific antigen progression. This set of genes may contribute to a better understanding of the molecular basis of prostate cancer. TCEB1 and SELC14L1 are good candidate markers for predicting prognosis and progression of prostate cancer.
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Affiliation(s)
- Laia Agell
- Department of Pathology, Hospital del Mar-Mar Health Park, Barcelona, Spain
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Prat-Vidal C, Gálvez-Montón C, Nonell L, Puigdecanet E, Astier L, Solé F, Bayes-Genis A. Identification of temporal and region-specific myocardial gene expression patterns in response to infarction in swine. PLoS One 2013; 8:e54785. [PMID: 23372767 PMCID: PMC3556027 DOI: 10.1371/journal.pone.0054785] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [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: 07/26/2012] [Accepted: 12/14/2012] [Indexed: 11/19/2022] Open
Abstract
Molecular mechanisms associated with pathophysiological changes in ventricular remodelling due to myocardial infarction (MI) remain poorly understood. We analyzed changes in gene expression by microarray technology in porcine myocardial tissue at 1, 4, and 6 weeks post-MI.MI was induced by coronary artery ligation in 9 female pigs (30-40 kg). Animals were randomly sacrificed at 1, 4, or 6 weeks post-MI (n = 3 per group) and 3 healthy animals were also included as control group. Total RNA from myocardial samples was hybridized to GeneChip® Porcine Genome Arrays. Functional analysis was obtained with the Ingenuity Pathway Analysis (IPA) online tool. Validation of microarray data was performed by quantitative real-time PCR (qRT-PCR).More than 8,000 different probe sets showed altered expression in the remodelling myocardium at 1, 4, or 6 weeks post-MI. Ninety-seven percent of altered transcripts were detected in the infarct core and 255 probe sets were differentially expressed in the remote myocardium. Functional analysis revealed 28 genes de-regulated in the remote myocardial region in at least one of the three temporal analyzed stages, including genes associated with heart failure (HF), systemic sclerosis and coronary artery disease. In the infarct core tissue, eight major time-dependent gene expression patterns were recognized among 4,221 probe sets commonly altered over time. Altered gene expression of ACVR2B, BID, BMP2, BMPR1A, LMNA, NFKBIA, SMAD1, TGFB3, TNFRSF1A, and TP53 were further validated.The clustering of similar expression patterns for gene products with related function revealed molecular footprints, some of them described for the first time, which elucidate changes in biological processes at different stages after MI.
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Affiliation(s)
- Cristina Prat-Vidal
- Imperial College Research Ethics Committee (Heart Failure and Cardiac Regeneration) Research Program, Health Sciences Research Institute Germans Trias i Pujol. Cardiology Service, Hospital Universitari Germans Trias i Pujol, Badalona (Barcelona), Spain
| | - Carolina Gálvez-Montón
- Imperial College Research Ethics Committee (Heart Failure and Cardiac Regeneration) Research Program, Health Sciences Research Institute Germans Trias i Pujol. Cardiology Service, Hospital Universitari Germans Trias i Pujol, Badalona (Barcelona), Spain
| | - Lara Nonell
- Servei d'Anàlisi de Microarrays, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Eulàlia Puigdecanet
- Servei d'Anàlisi de Microarrays, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Laura Astier
- Imperial College Research Ethics Committee (Heart Failure and Cardiac Regeneration) Research Program, Health Sciences Research Institute Germans Trias i Pujol. Cardiology Service, Hospital Universitari Germans Trias i Pujol, Badalona (Barcelona), Spain
| | - Francesc Solé
- Servei d'Anàlisi de Microarrays, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
- Laboratori de Citogenètica Molecular, Servei de Patologia, Hospital del Mar, Barcelona, Spain
| | - Antoni Bayes-Genis
- Imperial College Research Ethics Committee (Heart Failure and Cardiac Regeneration) Research Program, Health Sciences Research Institute Germans Trias i Pujol. Cardiology Service, Hospital Universitari Germans Trias i Pujol, Badalona (Barcelona), Spain
- Department of Medicine, University Autonomous of Barcelona, Barcelona, Spain
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Puiggros A, Puigdecanet E, Salido M, Ferrer A, Abella E, Gimeno E, Nonell L, Herranz MJ, Galván AB, Rodríguez-Rivera M, Melero C, Pairet S, Bellosillo B, Serrano S, Florensa L, Solé F, Espinet B. Genomic arrays in chronic lymphocytic leukemia routine clinical practice: are we ready to substitute conventional cytogenetics and fluorescence in situ hybridization techniques? Leuk Lymphoma 2012; 54:986-95. [PMID: 22994157 DOI: 10.3109/10428194.2012.731598] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is characterized by a highly variable clinical course. Del(11q) and del(17p), routinely studied by conventional G-banding cytogenetics (CGC) and fluorescence in situ hybridization (FISH), have been related to progression and shorter overall survival. Recently, array-based karyotyping has gained acceptance as a high-resolution new tool for detecting genomic imbalances. The aim of the present study was to compare genomic arrays with CGC and FISH to ascertain whether the current techniques could be substituted in routine procedures. We analyzed 70 patients with CLL using the Cytogenetics Whole-Genome 2.7M Array and CytoScan HD Array (Affymetrix), CGC and FISH with the classical CLL panel. Whereas 31.4% and 68.6% of patients presented abnormalities when studied by CGC and FISH, respectively, these rates increased when arrays were also analyzed (78.6% and 80%). Although abnormality detection is higher when arrays are applied, one case with del(11q) and three with del(17p) were missed by genomic arrays due to their limited sensitivity. We consider that the complete substitution of CGC and FISH by genomic arrays in routine laboratories could negatively affect the management of some patients harboring 11q or 17p deletions. In conclusion, genomic arrays are valid to detect known and novel genomic imbalances in CLL, but should be maintained as a complementary tool to the current techniques.
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Affiliation(s)
- Anna Puiggros
- Programa de Recerca en Càncer, Grup de Recerca Translacional en Neoplàsies Hematològiques (GRETNHE), IMIM-Hospital del Mar, Barcelona, Spain
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Comabella M, Lünemann JD, Río J, Sánchez A, López C, Julià E, Fernández M, Nonell L, Camiña-Tato M, Deisenhammer F, Caballero E, Tortola MT, Prinz M, Montalban X, Martin R. A type I interferon signature in monocytes is associated with poor response to interferon-beta in multiple sclerosis. ACTA ACUST UNITED AC 2010; 132:3353-65. [PMID: 19741051 DOI: 10.1093/brain/awp228] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The effect of interferon-beta in multiple sclerosis is modest and many patients do not respond to treatment. To date, no single biomarker reliably correlates with responsiveness to interferon-beta in multiple sclerosis. In the present study, genome-wide expression profiling was performed in peripheral blood mononuclear cells from 47 multiple sclerosis patients treated with interferon-beta for a minimum of 2 years and classified as responders and non-responders based on clinical criteria. A validation cohort of 30 multiple sclerosis patients was included in the study to replicate gene-expression findings. Before treatment, interferon-beta responders and non-responders were characterized by differential expression of type I interferon-induced genes with overexpression of the type interferon-induced genes in non-responders. Upon treatment the expression of these genes remained unaltered in non-responders, but was strongly upregulated in responders. Functional experiments showed a selective increase in phosphorylated STAT1 levels and interferon receptor 1 expression in monocytes of non-responders at baseline. When dissecting this type I interferon signature further, interferon-beta non-responders were characterized by increased monocyte type I interferon secretion upon innate immune stimuli via toll-like receptor 4, by increased endogenous production of type I interferon, and by an elevated activation status of myeloid dendritic cells. These findings indicate that perturbations of the type I interferon signalling pathway in monocytes are related to lack of response to interferon-beta, and type I interferon-regulated genes may be used as response markers in interferon-beta treatment.
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Affiliation(s)
- M Comabella
- Unitat de Neuroimmunologia Clínica, CEM-Cat. Edif. EUI 2 feminine planta, Hospital Universitari Vall d'Hebron, Pg. Vall d'Hebron 119-129, 08035 Barcelona, Spain.
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