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Atla G, Bonàs-Guarch S, Cuenca-Ardura M, Beucher A, Crouch DJM, Garcia-Hurtado J, Moran I, Irimia M, Prasad RB, Gloyn AL, Marselli L, Suleiman M, Berney T, de Koning EJP, Kerr-Conte J, Pattou F, Todd JA, Piemonti L, Ferrer J. Genetic regulation of RNA splicing in human pancreatic islets. Genome Biol 2022; 23:196. [PMID: 36109769 PMCID: PMC9479353 DOI: 10.1186/s13059-022-02757-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 08/23/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Non-coding genetic variants that influence gene transcription in pancreatic islets play a major role in the susceptibility to type 2 diabetes (T2D), and likely also contribute to type 1 diabetes (T1D) risk. For many loci, however, the mechanisms through which non-coding variants influence diabetes susceptibility are unknown. RESULTS We examine splicing QTLs (sQTLs) in pancreatic islets from 399 human donors and observe that common genetic variation has a widespread influence on the splicing of genes with established roles in islet biology and diabetes. In parallel, we profile expression QTLs (eQTLs) and use transcriptome-wide association as well as genetic co-localization studies to assign islet sQTLs or eQTLs to T2D and T1D susceptibility signals, many of which lack candidate effector genes. This analysis reveals biologically plausible mechanisms, including the association of T2D with an sQTL that creates a nonsense isoform in ERO1B, a regulator of ER-stress and proinsulin biosynthesis. The expanded list of T2D risk effector genes reveals overrepresented pathways, including regulators of G-protein-mediated cAMP production. The analysis of sQTLs also reveals candidate effector genes for T1D susceptibility such as DCLRE1B, a senescence regulator, and lncRNA MEG3. CONCLUSIONS These data expose widespread effects of common genetic variants on RNA splicing in pancreatic islets. The results support a role for splicing variation in diabetes susceptibility, and offer a new set of genetic targets with potential therapeutic benefit.
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Affiliation(s)
- Goutham Atla
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en red Diabetes y enfermedades metabólicas asociadas (CIBERDEM), Barcelona, Spain
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Silvia Bonàs-Guarch
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Centro de Investigación Biomédica en red Diabetes y enfermedades metabólicas asociadas (CIBERDEM), Barcelona, Spain.
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
| | - Mirabai Cuenca-Ardura
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en red Diabetes y enfermedades metabólicas asociadas (CIBERDEM), Barcelona, Spain
| | - Anthony Beucher
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en red Diabetes y enfermedades metabólicas asociadas (CIBERDEM), Barcelona, Spain
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Daniel J M Crouch
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Javier Garcia-Hurtado
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en red Diabetes y enfermedades metabólicas asociadas (CIBERDEM), Barcelona, Spain
| | - Ignasi Moran
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Present Address: Life Sciences Department, Barcelona Supercomputing Center (BSC), 08034, Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rashmi B Prasad
- Lund University Diabetes Centre, Clinical Research Center, Malmö, Sweden
- Department of Clinical Sciences in Malmö, Lund University, Malmö, Sweden
| | - Anna L Gloyn
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Department of Pediatrics, Division of Endocrinology, Stanford School of Medicine, Stanford, CA, USA
| | - Lorella Marselli
- Department of Clinical and Experimental Medicine, AOUP Cisanello University Hospital, University of Pisa, Pisa, Italy
| | - Mara Suleiman
- Department of Clinical and Experimental Medicine, AOUP Cisanello University Hospital, University of Pisa, Pisa, Italy
| | - Thierry Berney
- Cell Isolation and Transplantation Center, University of Geneva, Geneva, Switzerland
| | - Eelco J P de Koning
- Department of Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Hubrecht Institute/KNAW, Utrecht, the Netherlands
| | - Julie Kerr-Conte
- University of Lille, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire de Lille (CHU Lille), Institute Pasteur Lille, U1190 -European Genomic Institute for Diabetes (EGID), F59000, Lille, France
| | - Francois Pattou
- University of Lille, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire de Lille (CHU Lille), Institute Pasteur Lille, U1190 -European Genomic Institute for Diabetes (EGID), F59000, Lille, France
| | - John A Todd
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Lorenzo Piemonti
- Diabetes Research Institute, IRCCS Ospedale San Raffaele and Università Vita-Salute San Raffaele, Milan, Italy
| | - Jorge Ferrer
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Centro de Investigación Biomédica en red Diabetes y enfermedades metabólicas asociadas (CIBERDEM), Barcelona, Spain.
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
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2
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Ghose R, Aranguren-Ibáñez Á, Arecco N, Balboa D, Bataller M, Beltran S, Benisty H, Bénard A, Bernardo E, Carbonell Sala S, Casals E, Ciampi L, Condemi L, Corvó A, Cosín-Tomás M, Cuenca-Ardura M, Duran Serrano JM, Espejo Díaz MI, Fernandez Callejo M, Gañez-Zapater A, Garcia-Castellanos R, Garrido R, Henkin G, Hermoso Pulido T, Hernandez-Alias X, Herrero Vicente J, Ingham M, Lim WM, Llonch S, Marmesat Bertoli E, Miguel-Escalada I, Montero-Blay A, Navarrete Hernández C, Neguembor MV, Ní Chárthaigh RA, Pardo-Lorente N, Pascual-Reguant L, Pérez-Lluch S, Perza R, Pesaresi M, Picó Amador D, Pifarré P, Piscia D, Plana-Carmona M, Ponomarenko J, Radusky L, Rivero E, Rogalska M, Torcal Garcia G, Wojnacki J. From research to rapid response: mass COVID-19 testing by volunteers at the Centre for Genomic Regulation. F1000Res 2021; 9:1336. [PMID: 34745570 PMCID: PMC8564741 DOI: 10.12688/f1000research.27497.1] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/04/2020] [Indexed: 11/20/2022] Open
Abstract
The COVID-19 pandemic has posed and is continuously posing enormous societal and health challenges worldwide. The research community has mobilized to develop novel projects to find a cure or a vaccine, as well as to contribute to mass testing, which has been a critical measure to contain the infection in several countries. Through this article, we share our experiences and learnings as a group of volunteers at the Centre for Genomic Regulation (CRG) in Barcelona, Spain. As members of the ORFEU project, an initiative by the Government of Catalonia to achieve mass testing of people at risk and contain the epidemic in Spain, we share our motivations, challenges and the key lessons learnt, which we feel will help better prepare the global society to address similar situations in the future.
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Affiliation(s)
- Ritobrata Ghose
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, 08005, Spain
| | - Álvaro Aranguren-Ibáñez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Niccolò Arecco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Diego Balboa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Marc Bataller
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
| | - Hannah Benisty
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Angèle Bénard
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Edgar Bernardo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Sílvia Carbonell Sala
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Eloi Casals
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
| | - Ludovica Ciampi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Livia Condemi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Alberto Corvó
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
| | - Marta Cosín-Tomás
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,ISGlobal, Barcelona, 08036, Spain.,CIBER de Epidemiología y Salud Pública, Barcelona, 08023, Spain
| | - Mirabai Cuenca-Ardura
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Juan Manuel Duran Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - María Isabel Espejo Díaz
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Marcos Fernandez Callejo
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
| | - Antoni Gañez-Zapater
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Raquel Garcia-Castellanos
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Romina Garrido
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Gil Henkin
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Toni Hermoso Pulido
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Xavier Hernandez-Alias
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Jorge Herrero Vicente
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Matthew Ingham
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
| | - Wei Ming Lim
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Sílvia Llonch
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Elena Marmesat Bertoli
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
| | - Irene Miguel-Escalada
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Ariadna Montero-Blay
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Cristina Navarrete Hernández
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Róisín-Ana Ní Chárthaigh
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Natalia Pardo-Lorente
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Laura Pascual-Reguant
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Sílvia Pérez-Lluch
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Reyes Perza
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Martina Pesaresi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Daniel Picó Amador
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
| | - Paula Pifarré
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Davide Piscia
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
| | - Marcos Plana-Carmona
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Julia Ponomarenko
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Leandro Radusky
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Ezequiel Rivero
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Malgorzata Rogalska
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Guillem Torcal Garcia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - José Wojnacki
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
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3
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Richart L, Lapi E, Pancaldi V, Cuenca-Ardura M, Pau ECDS, Madrid-Mencía M, Neyret-Kahn H, Radvanyi F, Rodríguez JA, Cuartero Y, Serra F, Le Dily F, Valencia A, Marti-Renom MA, Real FX. STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells. Nucleic Acids Res 2021; 49:11005-11021. [PMID: 34648034 PMCID: PMC8565347 DOI: 10.1093/nar/gkab864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 09/08/2021] [Accepted: 09/29/2021] [Indexed: 12/13/2022] Open
Abstract
Cohesin exists in two variants containing STAG1 or STAG2. STAG2 is one of the most mutated genes in cancer and a major bladder tumor suppressor. Little is known about how its inactivation contributes to tumorigenesis. Here, we analyze the genomic distribution of STAG1 and STAG2 and perform STAG2 loss-of-function experiments using RT112 bladder cancer cells; we then analyze the genomic effects by integrating gene expression and chromatin interaction data. Functional compartmentalization exists between the cohesin complexes: cohesin-STAG2 displays a distinctive genomic distribution and mediates short and mid-ranged interactions that engage genes at higher frequency than those established by cohesin-STAG1. STAG2 knockdown results in down-regulation of the luminal urothelial signature and up-regulation of the basal transcriptional program, mirroring differences between STAG2-high and STAG2-low human bladder tumors. This is accompanied by rewiring of DNA contacts within topological domains, while compartments and domain boundaries remain refractive. Contacts lost upon depletion of STAG2 are assortative, preferentially occur within silent chromatin domains, and are associated with de-repression of lineage-specifying genes. Our findings indicate that STAG2 participates in the DNA looping that keeps the basal transcriptional program silent and thus sustains the luminal program. This mechanism may contribute to the tumor suppressor function of STAG2 in the urothelium.
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Affiliation(s)
- Laia Richart
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Eleonora Lapi
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain.,Center for Biomedical Research Network (CIBERONC), 28029 Madrid, Spain
| | - Vera Pancaldi
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain.,Centre de Recherches en Cancérologie de Toulouse (CRCT), UMR1037 Inserm, ERL5294 CNRS, 31037 Toulouse, France.,University Paul Sabatier III, Toulouse, France
| | - Mirabai Cuenca-Ardura
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | | | - Miguel Madrid-Mencía
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain.,Centre de Recherches en Cancérologie de Toulouse (CRCT), UMR1037 Inserm, ERL5294 CNRS, 31037 Toulouse, France.,University Paul Sabatier III, Toulouse, France
| | - Hélène Neyret-Kahn
- Institut Curie, PSL Research University, CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, 75005 Paris, France.,Sorbonne Université, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France
| | - François Radvanyi
- Institut Curie, PSL Research University, CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, 75005 Paris, France.,Sorbonne Université, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France
| | - Juan Antonio Rodríguez
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Yasmina Cuartero
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - François Serra
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - François Le Dily
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Marc A Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.,Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain.,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain.,Center for Biomedical Research Network (CIBERONC), 28029 Madrid, Spain.,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
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