1
|
Kathami N, Moreno-Vicente C, Martín P, Vergara-Arce JA, Ruiz-Hernández R, Gerovska D, Aransay AM, Araúzo-Bravo MJ, Camarero-Espinosa S, Abarrategi A. rhBMP-2 induces terminal differentiation of human bone marrow mesenchymal stromal cells only by synergizing with other signals. Stem Cell Res Ther 2024; 15:124. [PMID: 38679735 PMCID: PMC11057131 DOI: 10.1186/s13287-024-03735-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/17/2024] [Indexed: 05/01/2024] Open
Abstract
BACKGROUND Recombinant human bone morphogenetic protein 2 (rhBMP-2) and human bone marrow mesenchymal stromal cells (hBM-MSCs) have been thoroughly studied for research and translational bone regeneration purposes. rhBMP-2 induces bone formation in vivo, and hBM-MSCs are its target, bone-forming cells. In this article, we studied how rhBMP-2 drives the multilineage differentiation of hBM-MSCs both in vivo and in vitro. METHODS rhBMP-2 and hBM-MSCs were tested in an in vivo subcutaneous implantation model to assess their ability to form mature bone and undergo multilineage differentiation. Then, the hBM-MSCs were treated in vitro with rhBMP-2 for short-term or long-term cell-culture periods, alone or in combination with osteogenic, adipogenic or chondrogenic media, aiming to determine the role of rhBMP-2 in these differentiation processes. RESULTS The data indicate that hBM-MSCs respond to rhBMP-2 in the short term but fail to differentiate in long-term culture conditions; these cells overexpress the rhBMP-2 target genes DKK1, HEY-1 and SOST osteogenesis inhibitors. However, in combination with other differentiation signals, rhBMP-2 acts as a potentiator of multilineage differentiation, not only of osteogenesis but also of adipogenesis and chondrogenesis, both in vitro and in vivo. CONCLUSIONS Altogether, our data indicate that rhBMP-2 alone is unable to induce in vitro osteogenic terminal differentiation of hBM-MSCs, but synergizes with other signals to potentiate multiple differentiation phenotypes. Therefore, rhBMP-2 triggers on hBM-MSCs different specific phenotype differentiation depending on the signalling environment.
Collapse
Affiliation(s)
- Neda Kathami
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), 20014, Donostia-San Sebastian, Spain
- POLYMAT, University of the Basque Country (UPV-EHU), 20018, Donostia-San Sebastian, Spain
| | | | - Pablo Martín
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), 20014, Donostia-San Sebastian, Spain
| | - Jhonatan A Vergara-Arce
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), 20014, Donostia-San Sebastian, Spain
| | - Raquel Ruiz-Hernández
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), 20014, Donostia-San Sebastian, Spain
| | - Daniela Gerovska
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014, San Sebastián, Spain
| | - Ana M Aransay
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160, Derio, Spain
- Centro de Investigación Biomedica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Marcos J Araúzo-Bravo
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014, San Sebastián, Spain
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of Basque Country (UPV/EHU), 48940, Leioa, Spain
- IKERBASQUE, Basque Foundation for Science, 48009, Bilbao, Spain
| | - Sandra Camarero-Espinosa
- POLYMAT, University of the Basque Country (UPV-EHU), 20018, Donostia-San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science, 48009, Bilbao, Spain
| | - Ander Abarrategi
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), 20014, Donostia-San Sebastian, Spain.
- IKERBASQUE, Basque Foundation for Science, 48009, Bilbao, Spain.
- Regenerative Medicine and Disease Models Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Paseo Miramón, 194, 20014, Donostia, Gipuzkoa, Spain.
| |
Collapse
|
2
|
Martin-Martin C, Suarez-Alvarez B, González M, Torres IB, Bestard O, Martín JE, Barceló-Coblijn G, Moreso F, Aransay AM, Lopez-Larrea C, Rodriguez RM. Exploring kidney allograft rejection: A proof-of-concept study using spatial transcriptomics. Am J Transplant 2024:S1600-6135(24)00287-9. [PMID: 38692412 DOI: 10.1016/j.ajt.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/03/2024]
Abstract
In this proof-of-concept study, spatial transcriptomics combined with public single-cell RNA-sequencing data were used to explore the potential of this technology to study kidney allograft rejection. We aimed to map gene expression patterns within diverse pathological states by examining biopsies classified across non-rejection, T cell-mediated acute rejection, and interstitial fibrosis and tubular atrophy (IFTA). Our results revealed distinct immune cell signatures, including those of T and B lymphocytes, monocytes, mast cells, and plasma cells, and their spatial organization within the renal interstitium. We also mapped chemokine receptors and ligands to study immune-cell migration and recruitment. Finally, our analysis demonstrated differential spatial enrichment of transcription signatures associated with kidney allograft rejection across various biopsy regions. Interstitium regions displayed higher enrichment scores for rejection-associated gene expression patterns than did tubular areas, which had negative scores. This implies that these signatures are primarily driven by processes unfolding in the renal interstitium. Overall, this study highlights the value of spatial transcriptomics for revealing cellular heterogeneity and immune signatures in renal transplant biopsies, and demonstrates its potential for studying the molecular and cellular mechanisms associated with rejection. However, certain limitations must be borne in mind regarding the development and future applications of this technology.
Collapse
Affiliation(s)
- Cristina Martin-Martin
- Translational Immunology, Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain; RICORS2040, Madrid, Spain
| | - Beatriz Suarez-Alvarez
- Translational Immunology, Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain; RICORS2040, Madrid, Spain
| | - Monika González
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain
| | - Irina B Torres
- Department of Nephrology, Hospital Universitari Vall d'Hebron, Nephrology and Renal Transplant Laboratory. Vall Hebron Research Institute (VHIR). Department of Medicine. Autonomous University of Barcelona. Barcelona, Spain
| | - Oriol Bestard
- Department of Nephrology, Hospital Universitari Vall d'Hebron, Nephrology and Renal Transplant Laboratory. Vall Hebron Research Institute (VHIR). Department of Medicine. Autonomous University of Barcelona. Barcelona, Spain
| | - José E Martín
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain
| | - Gwendolyn Barceló-Coblijn
- Lipids in Human Pathology, Institut d'Investigació Sanitària Illes Balears (IdISBa), Ctra. Valldemossa 79, E-07120 Palma, Balearic Islands, Spain; Research Unit, University Hospital Son Espases, Ctra. Valldemossa79, E-07120 Palma, Balearic Islands, Spain
| | - Francesc Moreso
- Department of Nephrology, Hospital Universitari Vall d'Hebron, Nephrology and Renal Transplant Laboratory. Vall Hebron Research Institute (VHIR). Department of Medicine. Autonomous University of Barcelona. Barcelona, Spain
| | - Ana M Aransay
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Carlos Lopez-Larrea
- Translational Immunology, Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain; RICORS2040, Madrid, Spain; Department of Immunology, Hospital Universitario Central de Asturias, 33011, Oviedo, Spain.
| | - Ramon M Rodriguez
- Lipids in Human Pathology, Institut d'Investigació Sanitària Illes Balears (IdISBa), Ctra. Valldemossa 79, E-07120 Palma, Balearic Islands, Spain; Research Unit, University Hospital Son Espases, Ctra. Valldemossa79, E-07120 Palma, Balearic Islands, Spain
| |
Collapse
|
3
|
Ayuso-García P, Sánchez-Rueda A, Velasco-Avilés S, Tamayo-Caro M, Ferrer-Pinós A, Huarte-Sebastian C, Alvarez V, Riobello C, Jiménez-Vega S, Buendia I, Cañas-Martin J, Fernández-Susavila H, Aparicio-Rey A, Esquinas-Román EM, Ponte CR, Guhl R, Laville N, Pérez-Andrés E, Lavín JL, González-Lopez M, Cámara NM, Aransay AM, Lozano JJ, Sutherland JD, Barrio R, Martinez-Chantar ML, Azkargorta M, Elortza F, Soriano-Navarro M, Matute C, Sánchez-Gómez MV, Bayón-Cordero L, Pérez-Samartín A, Bravo SB, Kurz T, Lama-Díaz T, Blanco MG, Haddad S, Record CJ, van Hasselt PM, Reilly MM, Varela-Rey M, Woodhoo A. Neddylation orchestrates the complex transcriptional and posttranscriptional program that drives Schwann cell myelination. Sci Adv 2024; 10:eadm7600. [PMID: 38608019 PMCID: PMC11014456 DOI: 10.1126/sciadv.adm7600] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 03/11/2024] [Indexed: 04/14/2024]
Abstract
Myelination is essential for neuronal function and health. In peripheral nerves, >100 causative mutations have been identified that cause Charcot-Marie-Tooth disease, a disorder that can affect myelin sheaths. Among these, a number of mutations are related to essential targets of the posttranslational modification neddylation, although how these lead to myelin defects is unclear. Here, we demonstrate that inhibiting neddylation leads to a notable absence of peripheral myelin and axonal loss both in developing and regenerating mouse nerves. Our data indicate that neddylation exerts a global influence on the complex transcriptional and posttranscriptional program by simultaneously regulating the expression and function of multiple essential myelination signals, including the master transcription factor EGR2 and the negative regulators c-Jun and Sox2, and inducing global secondary changes in downstream pathways, including the mTOR and YAP/TAZ signaling pathways. This places neddylation as a critical regulator of myelination and delineates the potential pathogenic mechanisms involved in CMT mutations related to neddylation.
Collapse
Affiliation(s)
- Paula Ayuso-García
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Alejandro Sánchez-Rueda
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Sergio Velasco-Avilés
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Miguel Tamayo-Caro
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Aroa Ferrer-Pinós
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Cecilia Huarte-Sebastian
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Vanesa Alvarez
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Cristina Riobello
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Selene Jiménez-Vega
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Izaskun Buendia
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
- Laboratory of Neurobiology, Achucarro Basque Center for Neuroscience, Science Park of UPV/EHU, Sede building, 48940 Leioa, Spain
| | - Jorge Cañas-Martin
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Héctor Fernández-Susavila
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Adrián Aparicio-Rey
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Eva M. Esquinas-Román
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Carlos Rodríguez Ponte
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
| | - Romane Guhl
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
- Université Paris Cité Magistère Européen de Génétique, 85 Boulevard Saint-Germain, 75006 Paris, France
| | - Nicolas Laville
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
- Université Paris Cité Magistère Européen de Génétique, 85 Boulevard Saint-Germain, 75006 Paris, France
| | - Encarni Pérez-Andrés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - José L. Lavín
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
- NEIKER–Basque Institute for Agricultural Research and Development, Applied Mathematics Department, Bioinformatics Unit, Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Monika González-Lopez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Nuria Macías Cámara
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Ana M. Aransay
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan José Lozano
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - James D. Sutherland
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - María Luz Martinez-Chantar
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Mikel Azkargorta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Félix Elortza
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Mario Soriano-Navarro
- Electron Microscopy Core Facility, Centro de Investigación Príncipe Felipe (CIPF), 46012 Valencia, Spain
| | - Carlos Matute
- Laboratory of Neurobiology, Achucarro Basque Center for Neuroscience, Science Park of UPV/EHU, Sede building, 48940 Leioa, Spain
- Department of Neurosciences, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - María Victoria Sánchez-Gómez
- Laboratory of Neurobiology, Achucarro Basque Center for Neuroscience, Science Park of UPV/EHU, Sede building, 48940 Leioa, Spain
- Department of Neurosciences, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Laura Bayón-Cordero
- Laboratory of Neurobiology, Achucarro Basque Center for Neuroscience, Science Park of UPV/EHU, Sede building, 48940 Leioa, Spain
- Department of Neurosciences, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Alberto Pérez-Samartín
- Laboratory of Neurobiology, Achucarro Basque Center for Neuroscience, Science Park of UPV/EHU, Sede building, 48940 Leioa, Spain
- Department of Neurosciences, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Susana B. Bravo
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), 15705 Santiago de Compostela, A Coruña, Spain
| | - Thimo Kurz
- Evotec SE, Innovation Dr, Milton, Abingdon OX14 4RT, UK and School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Tomas Lama-Díaz
- DNA Repair and Genome Integrity Laboratory, CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria, 15706 Santiago de Compostela, A Coruña, Spain
| | - Miguel G. Blanco
- DNA Repair and Genome Integrity Laboratory, CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria, 15706 Santiago de Compostela, A Coruña, Spain
- Department of Biochemistry and Molecular Biology, University of Santiago de Compostela, Plaza do Obradoiro s/n, Santiago de Compostela, Spain
| | - Saif Haddad
- Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Christopher J. Record
- Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Peter M. van Hasselt
- Department of Metabolic Diseases, Division Pediatrics, Wilhelmina Children’s Hospital University Medical Center Utrecht, Utrecht University, 3584 EA, Utrecht, Netherlands
| | - Mary M. Reilly
- Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Marta Varela-Rey
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
- Department of Biochemistry and Molecular Biology, University of Santiago de Compostela, Plaza do Obradoiro s/n, Santiago de Compostela, Spain
| | - Ashwin Woodhoo
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, A Coruña, Spain
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Bizkaia, Spain
- Department of Functional Biology, University of Santiago de Compostela, Plaza do Obradoiro s/n, Santiago de Compostela, Spain
- Oportunius Research Professor at CIMUS/USC, Galician Agency of Innovation (GAIN), Xunta de Galicia, Santiago de Compostela, A Coruña, Spain
| |
Collapse
|
4
|
Lachiondo-Ortega S, Rejano-Gordillo CM, Simon J, Lopitz-Otsoa F, C Delgado T, Mazan-Mamczarz K, Goikoetxea-Usandizaga N, Zapata-Pavas LE, García-Del Río A, Guerra P, Peña-Sanfélix P, Hermán-Sánchez N, Al-Abdulla R, Fernandez-Rodríguez C, Azkargorta M, Velázquez-Cruz A, Guyon J, Martín C, Zalamea JD, Egia-Mendikute L, Sanz-Parra A, Serrano-Maciá M, González-Recio I, Gonzalez-Lopez M, Martínez-Cruz LA, Pontisso P, Aransay AM, Barrio R, Sutherland JD, Abrescia NGA, Elortza F, Lujambio A, Banales JM, Luque RM, Gahete MD, Palazón A, Avila MA, G Marin JJ, De S, Daubon T, Díaz-Quintana A, Díaz-Moreno I, Gorospe M, Rodríguez MS, Martínez-Chantar ML. SUMOylation controls Hu antigen R posttranscriptional activity in liver cancer. Cell Rep 2024; 43:113924. [PMID: 38507413 PMCID: PMC11025316 DOI: 10.1016/j.celrep.2024.113924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 08/08/2023] [Accepted: 02/21/2024] [Indexed: 03/22/2024] Open
Abstract
The posttranslational modification of proteins critically influences many biological processes and is a key mechanism that regulates the function of the RNA-binding protein Hu antigen R (HuR), a hub in liver cancer. Here, we show that HuR is SUMOylated in the tumor sections of patients with hepatocellular carcinoma in contrast to the surrounding tissue, as well as in human cell line and mouse models of the disease. SUMOylation of HuR promotes major cancer hallmarks, namely proliferation and invasion, whereas the absence of HuR SUMOylation results in a senescent phenotype with dysfunctional mitochondria and endoplasmic reticulum. Mechanistically, SUMOylation induces a structural rearrangement of the RNA recognition motifs that modulates HuR binding affinity to its target RNAs, further modifying the transcriptomic profile toward hepatic tumor progression. Overall, SUMOylation constitutes a mechanism of HuR regulation that could be potentially exploited as a therapeutic strategy for liver cancer.
Collapse
Affiliation(s)
- Sofia Lachiondo-Ortega
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Claudia M Rejano-Gordillo
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Extremadura, University Institute of Biosanitary Research of Extremadura (INUBE), 06071 Badajoz, Spain; Biofisika Institute, Consejo Superior de Investigaciones Científicas (CSIC), Departamento Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Leioa, Spain
| | - Jorge Simon
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain
| | - Fernando Lopitz-Otsoa
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Teresa C Delgado
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Krystyna Mazan-Mamczarz
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA), Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Naroa Goikoetxea-Usandizaga
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - L Estefanía Zapata-Pavas
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Ana García-Del Río
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Pietro Guerra
- Unit of Internal Medicine and Hepatology (UIMH), Department of Medicine (DIMED), University of Padova, 35128 Padua, Italy
| | - Patricia Peña-Sanfélix
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Natalia Hermán-Sánchez
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), Department of Cell Biology, Physiology and Immunology of University of Córdoba, Reina Sofia University Hospital, CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), 14004 Córdoba, Spain
| | - Ruba Al-Abdulla
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universidad Miguel Hernández, Elche, Spain; Institute of Medical Biochemistry and Molecular Biology, University Medicine of Greifswald, 17475 Greifswald, Germany
| | - Carmen Fernandez-Rodríguez
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Mikel Azkargorta
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Proteomics Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Carlos III Networked Proteomics Platform (ProteoRed-ISCIII), 48160 Derio, Bizkaia, Spain
| | - Alejandro Velázquez-Cruz
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Joris Guyon
- University of Bordeaux, INSERM, BPH, U1219, 33000 Bordeaux, France; CHU de Bordeaux, Service de Pharmacologie Médicale, 33000 Bordeaux, France
| | - César Martín
- Biofisika Institute, Consejo Superior de Investigaciones Científicas (CSIC), Departamento Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Leioa, Spain
| | - Juan Diego Zalamea
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Leire Egia-Mendikute
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Arantza Sanz-Parra
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Marina Serrano-Maciá
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Irene González-Recio
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Monika Gonzalez-Lopez
- Genome Analysis Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Luis Alfonso Martínez-Cruz
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Patrizia Pontisso
- Unit of Internal Medicine and Hepatology (UIMH), Department of Medicine (DIMED), University of Padova, 35128 Padua, Italy
| | - Ana M Aransay
- Genome Analysis Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Rosa Barrio
- Ubiquitin-likes and Development Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - James D Sutherland
- Ubiquitin-likes and Development Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Nicola G A Abrescia
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Félix Elortza
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Proteomics Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Carlos III Networked Proteomics Platform (ProteoRed-ISCIII), 48160 Derio, Bizkaia, Spain
| | - Amaia Lujambio
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jesus M Banales
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain; Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain; Department of Biochemistry and Genetics, School of Sciences, University of Navarra, Pamplona, Spain
| | - Raúl M Luque
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), Department of Cell Biology, Physiology and Immunology of University of Córdoba, Reina Sofia University Hospital, CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), 14004 Córdoba, Spain
| | - Manuel D Gahete
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), Department of Cell Biology, Physiology and Immunology of University of Córdoba, Reina Sofia University Hospital, CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), 14004 Córdoba, Spain
| | - Asís Palazón
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Matias A Avila
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Hepatology Program, Centro de Investigación Médica Aplicada (CIMA), University of Navarra, Pamplona, Spain; Instituto de Investigaciones Sanitarias de Navarra (IdiSNA), Pamplona, Spain
| | - Jose J G Marin
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Experimental Hepatology and Drug Targeting (HEVEPHARM), Instituto de Investigación Biomédica de Salamanca (IBSAL), University of Salamanca, Salamanca, Spain
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA), Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Thomas Daubon
- University of Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux, France
| | - Antonio Díaz-Quintana
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA), Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Manuel S Rodríguez
- Laboratoire de Chimie de Coordination (LCC), UPR 8241, CNRS; IPBS-University of Toulouse III-Paul Sabatier, Toulouse, France
| | - María Luz Martínez-Chantar
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain.
| |
Collapse
|
5
|
D’Ambrosi S, García-Vílchez R, Kedra D, Vitali P, Macias-Cámara N, Bárcena L, Gonzalez-Lopez M, Aransay AM, Dietmann S, Hurtado A, Blanco S. Global and single-nucleotide resolution detection of 7-methylguanosine in RNA. RNA Biol 2024; 21:1-18. [PMID: 38566310 PMCID: PMC10993922 DOI: 10.1080/15476286.2024.2337493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2024] [Indexed: 04/04/2024] Open
Abstract
RNA modifications, including N-7-methylguanosine (m7G), are pivotal in governing RNA stability and gene expression regulation. The accurate detection of internal m7G modifications is of paramount significance, given recent associations between altered m7G deposition and elevated expression of the methyltransferase METTL1 in various human cancers. The development of robust m7G detection techniques has posed a significant challenge in the field of epitranscriptomics. In this study, we introduce two methodologies for the global and accurate identification of m7G modifications in human RNA. We introduce borohydride reduction sequencing (Bo-Seq), which provides base resolution mapping of m7G modifications. Bo-Seq achieves exceptional performance through the optimization of RNA depurination and scission, involving the strategic use of high concentrations of NaBH4, neutral pH and the addition of 7-methylguanosine monophosphate (m7GMP) during the reducing reaction. Notably, compared to NaBH4-based methods, Bo-Seq enhances the m7G detection performance, and simplifies the detection process, eliminating the necessity for intricate chemical steps and reducing the protocol duration. In addition, we present an antibody-based approach, which enables the assessment of m7G relative levels across RNA molecules and biological samples, however it should be used with caution due to limitations associated with variations in antibody quality between batches. In summary, our novel approaches address the pressing need for reliable and accessible methods to detect RNA m7G methylation in human cells. These advancements hold the potential to catalyse future investigations in the critical field of epitranscriptomics, shedding light on the complex regulatory roles of m7G in gene expression and its implications in cancer biology.
Collapse
Affiliation(s)
- Silvia D’Ambrosi
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Raquel García-Vílchez
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Salamanca, Spain
| | - Darek Kedra
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, Salamanca, Spain
| | - Patrice Vitali
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Nuria Macias-Cámara
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Laura Bárcena
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Monika Gonzalez-Lopez
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Ana M. Aransay
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Sabine Dietmann
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Antonio Hurtado
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, Salamanca, Spain
| | - Sandra Blanco
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Salamanca, Spain
| |
Collapse
|
6
|
Valera PS, Plou J, García I, Astobiza I, Viera C, M. Aransay A, Martin JE, Sasselli IR, Carracedo A, Liz-Marzán LM. SERS analysis of cancer cell-secreted purines reveals a unique paracrine crosstalk in MTAP-deficient tumors. Proc Natl Acad Sci U S A 2023; 120:e2311674120. [PMID: 38109528 PMCID: PMC10756296 DOI: 10.1073/pnas.2311674120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/09/2023] [Indexed: 12/20/2023] Open
Abstract
The tumor microenvironment (TME) is a dynamic pseudoorgan that shapes the development and progression of cancers. It is a complex ecosystem shaped by interactions between tumor and stromal cells. Although the traditional focus has been on the paracrine communication mediated by protein messengers, recent attention has turned to the metabolic secretome in tumors. Metabolic enzymes, together with exchanged substrates and products, have emerged as potential biomarkers and therapeutic targets. However, traditional techniques for profiling secreted metabolites in complex cellular contexts are limited. Surface-enhanced Raman scattering (SERS) has emerged as a promising alternative due to its nontargeted nature and simplicity of operation. Although SERS has demonstrated its potential for detecting metabolites in biological settings, its application in deciphering metabolic interactions within multicellular systems like the TME remains underexplored. In this study, we introduce a SERS-based strategy to investigate the secreted purine metabolites of tumor cells lacking methylthioadenosine phosphorylase (MTAP), a common genetic event associated with poor prognosis in various cancers. Our SERS analysis reveals that MTAP-deficient cancer cells selectively produce methylthioadenosine (MTA), which is taken up and metabolized by fibroblasts. Fibroblasts exposed to MTA exhibit: i) molecular reprogramming compatible with cancer aggressiveness, ii) a significant production of purine derivatives that could be readily recycled by cancer cells, and iii) the capacity to secrete purine derivatives that induce macrophage polarization. Our study supports the potential of SERS for cancer metabolism research and reveals an unprecedented paracrine crosstalk that explains TME reprogramming in MTAP-deleted cancers.
Collapse
Affiliation(s)
- Pablo S. Valera
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián20014, Spain
- Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Donostia-San Sebastián20014, Spain
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio48160, Spain
- Departamento de Química Aplicada, Universidad del País Vasco/Euskal Herriko Universitatea (UPV/EHU), Donostia-San Sebastián20018, Spain
| | - Javier Plou
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián20014, Spain
- Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Donostia-San Sebastián20014, Spain
- Center for Cooperative Research in Nanoscience (CIC nanoGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián20018, Spain
| | - Isabel García
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián20014, Spain
- Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Donostia-San Sebastián20014, Spain
| | - Ianire Astobiza
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio48160, Spain
- Centro de Investigación Biomédica En Red de Cáncer (CIBERONC),Madrid28029, Spain
| | - Cristina Viera
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio48160, Spain
| | - Ana M. Aransay
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio48160, Spain
- Biomedical Research Networking Center in hepatic diseases, Derio48160, Spain
| | - José E. Martin
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio48160, Spain
| | - Ivan R. Sasselli
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián20014, Spain
- Centro de Fisica de Materiales, Consejo Superior de Investigaciones Cientificas-Universidad del País Vasco/Euskal Herriko Universitatea (CSIC-UPV)/EHU), Donostiarra-San Sebastián20018, Spain
| | - Arkaitz Carracedo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio48160, Spain
- Centro de Investigación Biomédica En Red de Cáncer (CIBERONC),Madrid28029, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao48009, Spain
- Translational Prostate Cancer Research Lab, Center for Cooperative Research in Biosciences-Basurto, Biocruces Bizkaia Health Research Institute, Derio48160, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad del País Vasco/Euskal Herriko Universitatea (UPV/EHU), Leioa48940, Spain
| | - Luis M. Liz-Marzán
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián20014, Spain
- Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Donostia-San Sebastián20014, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao48009, Spain
- Cinbio, Universidade de Vigo, Vigo36310, Spain
| |
Collapse
|
7
|
Baldan-Martin M, Rubín de Célix C, Orejudo M, Ortega Moreno L, Fernández-Tomé S, Soleto I, Ramirez C, Arroyo R, Fernández P, Santander C, Moreno-Monteagudo JA, Casanova MJ, Casals F, Casabona S, Becerro I, Lozano JJ, Aransay AM, Chaparro M, Gisbert JP. Long Non-Coding RNA Signatures in the Ileum and Colon of Crohn's Disease Patients and Effect of Anti-TNF-α Treatment on Their Modulation. Int J Mol Sci 2023; 24:15691. [PMID: 37958675 PMCID: PMC10650062 DOI: 10.3390/ijms242115691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
Biological therapies only benefit one-third of patients with Crohn's disease (CD). For this reason, a deeper understanding of the mechanisms by which biologics elicit their effect on intestinal mucosa is needed. Increasing evidence points toward the involvement of long noncoding RNAs (lncRNAs) in the pathogenesis of CD, although their role remains poorly studied. We aimed to characterize lncRNA profiles in the ileum and colon from CD patients and evaluate the effect of anti-TNF-α treatment on their transcription. Terminal ileum and left colon samples from 30 patients (active CD = 10, quiescent CD = 10, and healthy controls (HCs) = 10) were collected for RNA-seq. The patients were classified according to endoscopic activity. Furthermore, biopsies were cultured with infliximab, and their transcriptome was determined by Illumina gene expression array. A total of 678 differentially expressed lncRNAs between the terminal ileum and left colon were identified in HCs, 438 in patients with quiescent CD, and 468 in patients with active CD. Additionally, we identified three new lncRNAs in the ileum associated with CD activity. No differences were observed when comparing the effect of infliximab according to intestinal location, presence of disease (CD vs. HC), and activity (active vs. quiescent). The expression profiles of lncRNAs are associated with the location of intestinal tissue, being very different in the ileum and colon. The presence of CD and disease activity are associated with the differential expression of lncRNAs. No modulatory effect of infliximab has been observed in the lncRNA transcriptome.
Collapse
Affiliation(s)
- Montse Baldan-Martin
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Cristina Rubín de Célix
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Macarena Orejudo
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Lorena Ortega Moreno
- Área de Farmacología y Nutrición y Bromatología, Grupo de Investigación de Alto Rendimiento en Fisiopatología del Sistema Digestivo URJC: NeuGut-URJC, Departamento Ciencias Básicas de la Salud, Universidad Rey Juan Carlos, 28922 Madrid, Spain;
| | - Samuel Fernández-Tomé
- Departamento de Nutrición y Ciencia de los Alimentos, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain;
| | - Irene Soleto
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Cristina Ramirez
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Ricardo Arroyo
- Instituto de Medicina Molecular Aplicada Nemesio Díez (IMMA-ND), Facultad de Medicina, Universidad San Pablo CEU, 28668 Madrid, Spain (P.F.)
| | - Paloma Fernández
- Instituto de Medicina Molecular Aplicada Nemesio Díez (IMMA-ND), Facultad de Medicina, Universidad San Pablo CEU, 28668 Madrid, Spain (P.F.)
| | - Cecilio Santander
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - José Andrés Moreno-Monteagudo
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - María José Casanova
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Fernando Casals
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Sergio Casabona
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Irene Becerro
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Juan J. Lozano
- Bioinformatics Platform, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08036 Barcelona, Spain;
| | - Ana M. Aransay
- Genome Analysis Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Spain;
| | - María Chaparro
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Javier P. Gisbert
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| |
Collapse
|
8
|
García-del Río A, Prieto-Fernández E, Egia-Mendikute L, Antoñana-Vildosola A, Jimenez-Lasheras B, Lee SY, Barreira-Manrique A, Zanetti SR, de Blas A, Velasco-Beltrán P, Bosch A, Aransay AM, Palazon A. Factor-inhibiting HIF (FIH) promotes lung cancer progression. JCI Insight 2023; 8:e167394. [PMID: 37707961 PMCID: PMC10619494 DOI: 10.1172/jci.insight.167394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 09/12/2023] [Indexed: 09/16/2023] Open
Abstract
Factor-inhibiting HIF (FIH) is an asparagine hydroxylase that acts on hypoxia-inducible factors (HIFs) to control cellular adaptation to hypoxia. FIH is expressed in several tumor types, but its impact in tumor progression remains largely unexplored. We observed that FIH was expressed on human lung cancer tissue. Deletion of FIH in mouse and human lung cancer cells resulted in an increased glycolytic metabolism, consistent with increased HIF activity. FIH-deficient lung cancer cells exhibited decreased proliferation. Analysis of RNA-Seq data confirmed changes in the cell cycle and survival and revealed molecular pathways that were dysregulated in the absence of FIH, including the upregulation of angiomotin (Amot), a key component of the Hippo tumor suppressor pathway. We show that FIH-deficient tumors were characterized by higher immune infiltration of NK and T cells compared with FIH competent tumor cells. In vivo studies demonstrate that FIH deletion resulted in reduced tumor growth and metastatic capacity. Moreover, high FIH expression correlated with poor overall survival in non-small cell lung cancer (NSCLC). Our data unravel FIH as a therapeutic target for the treatment of lung cancer.
Collapse
Affiliation(s)
- Ana García-del Río
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Endika Prieto-Fernández
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Leire Egia-Mendikute
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Asier Antoñana-Vildosola
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Borja Jimenez-Lasheras
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - So Young Lee
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Adrián Barreira-Manrique
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Samanta Romina Zanetti
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Ander de Blas
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Paloma Velasco-Beltrán
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Alexandre Bosch
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Ana M. Aransay
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain
- Genome Analysis Platform, CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, Spain
| | - Asis Palazon
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| |
Collapse
|
9
|
Peña-Cearra A, Song D, Castelo J, Palacios A, Lavín JL, Azkargorta M, Elortza F, Fuertes M, Pascual-Itoiz MA, Barriales D, Martín-Ruiz I, Fullaondo A, Aransay AM, Rodríguez H, Palm NW, Anguita J, Abecia L. Mitochondrial dysfunction promotes microbial composition that negatively impacts on ulcerative colitis development and progression. NPJ Biofilms Microbiomes 2023; 9:74. [PMID: 37805634 PMCID: PMC10560208 DOI: 10.1038/s41522-023-00443-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 09/26/2023] [Indexed: 10/09/2023] Open
Abstract
Recent evidence demonstrates potential links between mitochondrial dysfunction and inflammatory bowel diseases (IBD). In addition, bidirectional interactions between the intestinal microbiota and host mitochondria may modulate intestinal inflammation. We observed previously that mice deficient in the mitochondrial protein MCJ (Methylation-controlled J protein) exhibit increased susceptibility to DSS colitis. However, it is unclear whether this phenotype is primarily driven by MCJ-/- associated gut microbiota dysbiosis or by direct effects of MCJ-deficiency. Here, we demonstrate that fecal microbiota transplantation (FMT) from MCJ-deficient into germ-free mice was sufficient to confer increased susceptibility to colitis. Therefore, an FMT experiment by cohousing was designed to alter MCJ-deficient microbiota. The phenotype resulting from complex I deficiency was reverted by FMT. In addition, we determined the protein expression pathways impacted by MCJ deficiency, providing insight into the pathophysiology of IBD. Further, we used magnetic activated cell sorting (MACS) and 16S rRNA gene sequencing to characterize taxa-specific coating of the intestinal microbiota with Immunoglobulin A (IgA-SEQ) in MCJ-deficient mice. We show that high IgA coating of fecal bacteria observed in MCJ-deficient mice play a potential role in disease progression. This study allowed us to identify potential microbial signatures in feces associated with complex I deficiency and disease progression. This research highlights the importance of finding microbial biomarkers, which might serve as predictors, permitting the stratification of ulcerative colitis (UC) patients into distinct clinical entities of the UC spectrum.
Collapse
Affiliation(s)
- Ainize Peña-Cearra
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park Bld 801 A, 48160, Derio, Spain
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48080, Bilbao, Spain
- Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48080, Bilbao, Spain
| | - Deguang Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, 06519 CT, USA
| | - Janire Castelo
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park Bld 801 A, 48160, Derio, Spain
| | - Ainhoa Palacios
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park Bld 801 A, 48160, Derio, Spain
| | - Jose Luis Lavín
- Applied Mathematics Department - Bioinformatics Unit, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, 48160, Derio, Spain
| | - Mikel Azkargorta
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park Bld 801 A, 48160, Derio, Spain
- CIBERehd, ISCIII, 28029, Madrid, Spain
- ProteoRed-ISCIII, 28029, Madrid, Spain
| | - Felix Elortza
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park Bld 801 A, 48160, Derio, Spain
- CIBERehd, ISCIII, 28029, Madrid, Spain
- ProteoRed-ISCIII, 28029, Madrid, Spain
| | - Miguel Fuertes
- Applied Mathematics Department - Bioinformatics Unit, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, 48160, Derio, Spain
| | - Miguel Angel Pascual-Itoiz
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park Bld 801 A, 48160, Derio, Spain
| | - Diego Barriales
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park Bld 801 A, 48160, Derio, Spain
| | - Itziar Martín-Ruiz
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park Bld 801 A, 48160, Derio, Spain
| | - Asier Fullaondo
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48080, Bilbao, Spain
| | - Ana M Aransay
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park Bld 801 A, 48160, Derio, Spain
- CIBERehd, ISCIII, 28029, Madrid, Spain
| | - Hector Rodríguez
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park Bld 801 A, 48160, Derio, Spain
| | - Noah W Palm
- Department of Immunobiology, Yale University School of Medicine, New Haven, 06519 CT, USA
| | - Juan Anguita
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park Bld 801 A, 48160, Derio, Spain.
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain.
| | - Leticia Abecia
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park Bld 801 A, 48160, Derio, Spain.
- Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48080, Bilbao, Spain.
| |
Collapse
|
10
|
García-Vílchez R, Añazco-Guenkova AM, López J, Dietmann S, Tomé M, Jimeno S, Azkargorta M, Elortza F, Bárcena L, Gonzalez-Lopez M, Aransay AM, Sánchez-Martín MA, Huertas P, Durán RV, Blanco S. N7-methylguanosine methylation of tRNAs regulates survival to stress in cancer. Oncogene 2023; 42:3169-3181. [PMID: 37660182 PMCID: PMC10589097 DOI: 10.1038/s41388-023-02825-0] [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: 09/12/2022] [Revised: 07/27/2023] [Accepted: 08/24/2023] [Indexed: 09/04/2023]
Abstract
Tumour progression and therapy tolerance are highly regulated and complex processes largely dependent on the plasticity of cancer cells and their capacity to respond to stress. The higher plasticity of cancer cells highlights the need for identifying targetable molecular pathways that challenge cancer cell survival. Here, we show that N7-guanosine methylation (m7G) of tRNAs, mediated by METTL1, regulates survival to stress conditions in cancer cells. Mechanistically, we find that m7G in tRNAs protects them from stress-induced cleavage and processing into 5' tRNA fragments. Our analyses reveal that the loss of tRNA m7G methylation activates stress response pathways, sensitising cancer cells to stress. Furthermore, we find that the loss of METTL1 reduces tumour growth and increases cytotoxic stress in vivo. Our study uncovers the role of m7G methylation of tRNAs in stress responses and highlights the potential of targeting METTL1 to sensitise cancer cells to chemotherapy.
Collapse
Affiliation(s)
- Raquel García-Vílchez
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Ana M Añazco-Guenkova
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Judith López
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Sabine Dietmann
- Washington University School of Medicine in St. Louis, 660S. Euclid Ave, St. Louis, MO, 63110, USA
| | - Mercedes Tomé
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Sevilla, Spain
| | - Sonia Jimeno
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain
| | - Mikel Azkargorta
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain
- Carlos III Networked Proteomics Platform (ProteoRed-ISCIII), Madrid, Spain
| | - Félix Elortza
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain
- Carlos III Networked Proteomics Platform (ProteoRed-ISCIII), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Laura Bárcena
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain
| | - Monika Gonzalez-Lopez
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain
| | - Ana M Aransay
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Manuel A Sánchez-Martín
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
- Servicio de Transgénesis, Nucleus, Universidad de Salamanca, 37007, Salamanca, Spain
| | - Pablo Huertas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain
| | - Raúl V Durán
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Sevilla, Spain
| | - Sandra Blanco
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain.
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain.
| |
Collapse
|
11
|
Capelo-Diz A, Lachiondo-Ortega S, Fernández-Ramos D, Cañas-Martín J, Goikoetxea-Usandizaga N, Serrano-Maciá M, González-Rellan MJ, Mosca L, Blazquez-Vicens J, Tinahones-Ruano A, Fondevila MF, Buyan M, Delgado TC, Gutierrez de Juan V, Ayuso-García P, Sánchez-Rueda A, Velasco-Avilés S, Fernández-Susavila H, Riobello-Suárez C, Dziechciarz B, Montiel-Duarte C, Lopitz-Otsoa F, Bizkarguenaga M, Bilbao-García J, Bernardo-Seisdedos G, Senra A, Soriano-Navarro M, Millet O, Díaz-Lagares Á, Crujeiras AB, Bao-Caamano A, Cabrera D, van Liempd S, Tamayo-Carro M, Borzacchiello L, Gomez-Santos B, Buqué X, Sáenz de Urturi D, González-Romero F, Simon J, Rodríguez-Agudo R, Ruiz A, Matute C, Beiroa D, Falcon-Perez JM, Aspichueta P, Rodríguez-Cuesta J, Porcelli M, Pajares MA, Ameneiro C, Fidalgo M, Aransay AM, Lama-Díaz T, Blanco MG, López M, Villa-Bellosta R, Müller TD, Nogueiras R, Woodhoo A, Martínez-Chantar ML, Varela-Rey M. Hepatic levels of S-adenosylmethionine regulate the adaptive response to fasting. Cell Metab 2023; 35:1373-1389.e8. [PMID: 37527658 PMCID: PMC10432853 DOI: 10.1016/j.cmet.2023.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 03/30/2023] [Accepted: 07/06/2023] [Indexed: 08/03/2023]
Abstract
There has been an intense focus to uncover the molecular mechanisms by which fasting triggers the adaptive cellular responses in the major organs of the body. Here, we show that in mice, hepatic S-adenosylmethionine (SAMe)-the principal methyl donor-acts as a metabolic sensor of nutrition to fine-tune the catabolic-fasting response by modulating phosphatidylethanolamine N-methyltransferase (PEMT) activity, endoplasmic reticulum-mitochondria contacts, β-oxidation, and ATP production in the liver, together with FGF21-mediated lipolysis and thermogenesis in adipose tissues. Notably, we show that glucagon induces the expression of the hepatic SAMe-synthesizing enzyme methionine adenosyltransferase α1 (MAT1A), which translocates to mitochondria-associated membranes. This leads to the production of this metabolite at these sites, which acts as a brake to prevent excessive β-oxidation and mitochondrial ATP synthesis and thereby endoplasmic reticulum stress and liver injury. This work provides important insights into the previously undescribed function of SAMe as a new arm of the metabolic adaptation to fasting.
Collapse
Affiliation(s)
- Alba Capelo-Diz
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, Santiago de Compostela, A Coruña 15706, Spain
| | - Sofía Lachiondo-Ortega
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - David Fernández-Ramos
- Precision Medicine and Metabolism Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain; Centro de investigación Biomedica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de salud Carlos III, 28029 Madrid, Spain
| | - Jorge Cañas-Martín
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, Santiago de Compostela, A Coruña 15706, Spain
| | - Naroa Goikoetxea-Usandizaga
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Marina Serrano-Maciá
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Maria J González-Rellan
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña 15706, Spain
| | - Laura Mosca
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via Luigi De Crecchio 7, 80138 Naples, Italy
| | - Joan Blazquez-Vicens
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, Santiago de Compostela, A Coruña 15706, Spain
| | - Alberto Tinahones-Ruano
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, Santiago de Compostela, A Coruña 15706, Spain
| | - Marcos F Fondevila
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña 15706, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Santiago de Compostela, A Coruña 15706, Spain
| | - Mason Buyan
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Teresa C Delgado
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Virginia Gutierrez de Juan
- Precision Medicine and Metabolism Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Paula Ayuso-García
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, Santiago de Compostela, A Coruña 15706, Spain
| | - Alejandro Sánchez-Rueda
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, Santiago de Compostela, A Coruña 15706, Spain
| | - Sergio Velasco-Avilés
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, Santiago de Compostela, A Coruña 15706, Spain
| | - Héctor Fernández-Susavila
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, Santiago de Compostela, A Coruña 15706, Spain
| | - Cristina Riobello-Suárez
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, Santiago de Compostela, A Coruña 15706, Spain
| | - Bartlomiej Dziechciarz
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, Santiago de Compostela, A Coruña 15706, Spain
| | - Cristina Montiel-Duarte
- The John van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, UK
| | - Fernando Lopitz-Otsoa
- Precision Medicine and Metabolism Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Maider Bizkarguenaga
- Precision Medicine and Metabolism Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Jon Bilbao-García
- Precision Medicine and Metabolism Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Ganeko Bernardo-Seisdedos
- Precision Medicine and Metabolism Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Ana Senra
- CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña 15706, Spain
| | - Mario Soriano-Navarro
- Electron Microscopy Core Facility, Centro de Investigación Príncipe Felipe (CIPF), Valencia 46012, Spain
| | - Oscar Millet
- Precision Medicine and Metabolism Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Ángel Díaz-Lagares
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, A Coruña 15706, Spain
| | - Ana B Crujeiras
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Santiago de Compostela, A Coruña 15706, Spain; Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), 15706 Santiago de Compostela, Spain
| | - Aida Bao-Caamano
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), 15706 Santiago de Compostela, Spain
| | - Diana Cabrera
- Metabolomics Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Sebastiaan van Liempd
- Metabolomics Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Miguel Tamayo-Carro
- Nerve Disorders Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Luigi Borzacchiello
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via Luigi De Crecchio 7, 80138 Naples, Italy
| | - Beatriz Gomez-Santos
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Xabier Buqué
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Diego Sáenz de Urturi
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Francisco González-Romero
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Jorge Simon
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Rubén Rodríguez-Agudo
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Asier Ruiz
- Laboratory of Neurobiology, Achucarro Basque Center for Neuroscience, Department of Neurosciences, University of Basque Country (UPV/EHU), Centro de investigación Biomedica en Red de Enfermedades Neurodegenerativas (CIBERNED), 48940 Leioa, Spain
| | - Carlos Matute
- Laboratory of Neurobiology, Achucarro Basque Center for Neuroscience, Department of Neurosciences, University of Basque Country (UPV/EHU), Centro de investigación Biomedica en Red de Enfermedades Neurodegenerativas (CIBERNED), 48940 Leioa, Spain
| | - Daniel Beiroa
- Experimental Biomedicine Center (CEBEGA), University of Santiago de Compostela, A Coruña 15706, Spain
| | - Juan M Falcon-Perez
- Centro de investigación Biomedica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de salud Carlos III, 28029 Madrid, Spain; Metabolomics Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia 48009, Spain
| | - Patricia Aspichueta
- Centro de investigación Biomedica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de salud Carlos III, 28029 Madrid, Spain; Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country UPV/EHU, Leioa, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Juan Rodríguez-Cuesta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Marina Porcelli
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via Luigi De Crecchio 7, 80138 Naples, Italy
| | - María A Pajares
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Cristina Ameneiro
- Stem Cells and Human Diseases, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña 15706, Spain
| | - Miguel Fidalgo
- Stem Cells and Human Diseases, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña 15706, Spain
| | - Ana M Aransay
- Genome Analysis Plataform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Tomas Lama-Díaz
- DNA Repair and Genome Integrity Laboratory, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña 15706, Spain
| | - Miguel G Blanco
- DNA Repair and Genome Integrity Laboratory, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña 15706, Spain; Department of Biochemistry and Molecular Biology, University of Santiago de Compostela, Plaza do Obradoiro s/n, Santiago de Compostela, Spain
| | - Miguel López
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña 15706, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Santiago de Compostela, A Coruña 15706, Spain
| | - Ricardo Villa-Bellosta
- Department of Biochemistry and Molecular Biology, University of Santiago de Compostela, Plaza do Obradoiro s/n, Santiago de Compostela, Spain; Metabolic Homeostasis and Vascular Calcification Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, A Coruña 15706, Spain
| | - Timo D Müller
- Institute for Diabetes and Obesity, Helmholtz Zentrum Munich, and German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Rubén Nogueiras
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña 15706, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Santiago de Compostela, A Coruña 15706, Spain; Oportunius Program, Galician Agency of Innovation (GAIN), Xunta de Galicia, Santiago de Compostela, A Coruña, Spain
| | - Ashwin Woodhoo
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, Santiago de Compostela, A Coruña 15706, Spain; Nerve Disorders Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia 48009, Spain; Oportunius Program, Galician Agency of Innovation (GAIN), Xunta de Galicia, Santiago de Compostela, A Coruña, Spain; Department of Functional Biology, University of Santiago de Compostela, Plaza do Obradoiro s/n, Santiago de Compostela, Spain
| | - María Luz Martínez-Chantar
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain; Centro de investigación Biomedica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de salud Carlos III, 28029 Madrid, Spain.
| | - Marta Varela-Rey
- Gene Regulatory Control in Disease Laboratory, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University of Santiago de Compostela, Santiago de Compostela, A Coruña 15706, Spain; Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain; Centro de investigación Biomedica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de salud Carlos III, 28029 Madrid, Spain; Department of Biochemistry and Molecular Biology, University of Santiago de Compostela, Plaza do Obradoiro s/n, Santiago de Compostela, Spain.
| |
Collapse
|
12
|
García-Vílchez R, Añazco-Guenkova AM, Dietmann S, López J, Morón-Calvente V, D'Ambrosi S, Nombela P, Zamacola K, Mendizabal I, García-Longarte S, Zabala-Letona A, Astobiza I, Fernández S, Paniagua A, Miguel-López B, Marchand V, Alonso-López D, Merkel A, García-Tuñón I, Ugalde-Olano A, Loizaga-Iriarte A, Lacasa-Viscasillas I, Unda M, Azkargorta M, Elortza F, Bárcena L, Gonzalez-Lopez M, Aransay AM, Di Domenico T, Sánchez-Martín MA, De Las Rivas J, Guil S, Motorin Y, Helm M, Pandolfi PP, Carracedo A, Blanco S. METTL1 promotes tumorigenesis through tRNA-derived fragment biogenesis in prostate cancer. Mol Cancer 2023; 22:119. [PMID: 37516825 PMCID: PMC10386714 DOI: 10.1186/s12943-023-01809-8] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 06/17/2023] [Indexed: 07/31/2023] Open
Abstract
Newly growing evidence highlights the essential role that epitranscriptomic marks play in the development of many cancers; however, little is known about the role and implications of altered epitranscriptome deposition in prostate cancer. Here, we show that the transfer RNA N7-methylguanosine (m7G) transferase METTL1 is highly expressed in primary and advanced prostate tumours. Mechanistically, we find that METTL1 depletion causes the loss of m7G tRNA methylation and promotes the biogenesis of a novel class of small non-coding RNAs derived from 5'tRNA fragments. 5'tRNA-derived small RNAs steer translation control to favour the synthesis of key regulators of tumour growth suppression, interferon pathway, and immune effectors. Knockdown of Mettl1 in prostate cancer preclinical models increases intratumoural infiltration of pro-inflammatory immune cells and enhances responses to immunotherapy. Collectively, our findings reveal a therapeutically actionable role of METTL1-directed m7G tRNA methylation in cancer cell translation control and tumour biology.
Collapse
Affiliation(s)
- Raquel García-Vílchez
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Ana M Añazco-Guenkova
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Sabine Dietmann
- Washington University School of Medicine in St. Louis, 660S. Euclid Ave, St. Louis, MO, 63110, USA
| | - Judith López
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Virginia Morón-Calvente
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Silvia D'Ambrosi
- Present Address: Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
| | - Paz Nombela
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Kepa Zamacola
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
| | - Isabel Mendizabal
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, 48011, Bilbao, Spain
| | - Saioa García-Longarte
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
| | - Amaia Zabala-Letona
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Ianire Astobiza
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Sonia Fernández
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Alejandro Paniagua
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
| | - Borja Miguel-López
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Virginie Marchand
- Université de Lorraine, UAR2008 IBSLor CNRS-UL-INSERM, Biopôle UL, 9, Avenue de La Forêt de Haye, 54505, Vandoeuvre-Les-Nancy, France
| | - Diego Alonso-López
- Bioinformatics Unit, Cancer Research Center (CIC-IBMCC, CSIC/USAL), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca (USAL), 37007, Salamanca, Spain
| | - Angelika Merkel
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916, Barcelona, Catalonia, Spain
- Germans Trias I Pujol Health Science Research Institute, Badalona, 08916, Barcelona, Catalonia, Spain
| | - Ignacio García-Tuñón
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
| | | | - Ana Loizaga-Iriarte
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Department of Urology, Basurto University Hospital, 48013, Bilbao, Spain
- Traslational Prostate Cancer Research Lab, CIC bioGUNE-Basurto, Biocruces Bizkaia Health Research Institute, Avenida Montevideo 18, 48013, Bilbao, Spain
| | | | - Miguel Unda
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Department of Urology, Basurto University Hospital, 48013, Bilbao, Spain
- Traslational Prostate Cancer Research Lab, CIC bioGUNE-Basurto, Biocruces Bizkaia Health Research Institute, Avenida Montevideo 18, 48013, Bilbao, Spain
| | - Mikel Azkargorta
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
- Carlos III Networked Proteomics Platform (ProteoRed-ISCIII), Madrid, Spain
| | - Félix Elortza
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
- Carlos III Networked Proteomics Platform (ProteoRed-ISCIII), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Laura Bárcena
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
| | - Monika Gonzalez-Lopez
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
| | - Ana M Aransay
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Tomás Di Domenico
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Manuel A Sánchez-Martín
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
- Servicio de Transgénesis, Nucleus, Universidad de Salamanca, 37007, Salamanca, Spain
| | - Javier De Las Rivas
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain
| | - Sònia Guil
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916, Barcelona, Catalonia, Spain
- Germans Trias I Pujol Health Science Research Institute, Badalona, 08916, Barcelona, Catalonia, Spain
| | - Yuri Motorin
- Université de Lorraine, UAR2008 IBSLor CNRS-UL-INSERM, Biopôle UL, 9, Avenue de La Forêt de Haye, 54505, Vandoeuvre-Les-Nancy, France
- Université de Lorraine, UMR7365 IMoPA CNRS-UL, Biopôle UL, 9, Avenue de La Forêt de Haye, 54505, Vandoeuvre-Les-Nancy, France
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Pier Paolo Pandolfi
- Molecular Biotechnology Center (MBC), Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126, Turin, TO, Italy
- William N. Pennington Cancer Center, Renown Health, Nevada System of Higher Education, Reno, NV, 89502, USA
| | - Arkaitz Carracedo
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, 48011, Bilbao, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Department of Pathology, Basurto University Hospital, 48013, Bilbao, Spain
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080, Bilbao, Spain
| | - Sandra Blanco
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007, Salamanca, Spain.
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain.
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 Bld, 48160, Derio, Bizkaia, Spain.
| |
Collapse
|
13
|
Cano A, Vazquez-Chantada M, Conde-Vancells J, Gonzalez-Lahera A, Mosen-Ansorena D, Blanco FJ, Clément K, Aron-Wisnewsky J, Tran A, Gual P, García-Monzón C, Caballería J, Castro A, Martínez-Chantar ML, Mato JM, Zhu H, Finnell RH, Aransay AM. Impaired Function of Solute Carrier Family 19 Leads to Low Folate Levels and Lipid Droplet Accumulation in Hepatocytes. Biomedicines 2023; 11:biomedicines11020337. [PMID: 36830876 PMCID: PMC9953281 DOI: 10.3390/biomedicines11020337] [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: 11/30/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
Low serum folate levels are inversely related to metabolic associated fatty liver disease (MAFLD). The role of the folate transporter gene (SLC19A1) was assessed to clarify its involvement in lipid accumulation during the onset of MAFLD in humans and in liver cells by genomic, transcriptomic, and metabolomic techniques. Genotypes of 3 SNPs in a case-control cohort were initially correlated to clinical and serum MAFLD markers. Subsequently, the expression of 84 key genes in response to the loss of SLC19A1 was evaluated with the aid of an RT2 profiler-array. After shRNA-silencing of SLC19A1 in THLE2 cells, folate and lipid levels were measured by ELISA and staining techniques, respectively. In addition, up to 482 amino acids and lipid metabolites were semi-quantified in SLC19A1-knockdown (KD) cells through ultra-high-performance liquid chromatography coupled with mass spectrometry. SNPs, rs1051266 and rs3788200, were significantly associated with the development of fatty liver for the single-marker allelic test. The minor alleles of these SNPs were associated with a 0.6/-1.67-fold decreased risk of developing MAFLD. When SLC19A1 was KD in THLE2 cells, intracellular folate content was four times lower than in wild-type cells. The lack of functional SLC19A1 provoked significant changes in the regulation of genes associated with lipid droplet accumulation within the cell and the onset of NAFLD. Metabolomic analyses showed a highly altered profile, where most of the species that accumulated in SLC19A1-KD-cells belong to the chemical groups of triacylglycerols, diacylglycerols, polyunsaturated fatty acids, and long chain, highly unsaturated cholesterol esters. In conclusion, the lack of SLC19A1 gene expression in hepatocytes affects the regulation of key genes for normal liver function, reduces intracellular folate levels, and impairs lipid metabolism, which entails lipid droplet accumulation in hepatocytes.
Collapse
Affiliation(s)
- Ainara Cano
- Food Research, AZTI, Basque Research and Technology Alliance (BRTA), Parque Tecnologico de Bizkaia, Astondo Bidea, Building 609, 48160 Derio, Spain
- OWL Metabolomics, Parque Tecnologico de Bizkaia, Building 502, 48160 Derio, Spain
| | - Mercedes Vazquez-Chantada
- OWL Metabolomics, Parque Tecnologico de Bizkaia, Building 502, 48160 Derio, Spain
- Department of Nutritional Sciences, Dell Paediatric Research Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Javier Conde-Vancells
- Department of Nutritional Sciences, Dell Paediatric Research Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Aintzane Gonzalez-Lahera
- CIC bioGUNE, Parque Tecnologico de Bizkaia, Building 801-A, 48160 Derio, Spain
- CIBERehd, ISCIII, 28029 Madrid, Spain
| | | | - Francisco J. Blanco
- CIC bioGUNE, Parque Tecnologico de Bizkaia, Building 801-A, 48160 Derio, Spain
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Karine Clément
- Nutriomics Research Group, Nutrition Department, Pitié-Salpétrière Hospital, INSERM, Sorbonne Université, F-75013 Paris, France
- INSERM, UMR_S 1166, NutriOmics Team 6, F-75013 Paris, France
- Assistance Publique Hôpitaux de Paris, Nutrition department ICAN and CRNH-Ile de France, Pitié-Salpêtrière Hospital, F-75013 Paris, France
| | - Judith Aron-Wisnewsky
- Nutriomics Research Group, Nutrition Department, Pitié-Salpétrière Hospital, INSERM, Sorbonne Université, F-75013 Paris, France
- INSERM, UMR_S 1166, NutriOmics Team 6, F-75013 Paris, France
- Assistance Publique Hôpitaux de Paris, Nutrition department ICAN and CRNH-Ile de France, Pitié-Salpêtrière Hospital, F-75013 Paris, France
| | - Albert Tran
- Team 8 “Chronic Liver Diseases Associated with Obesity and Alcohol”, INSERM, U1065, Centre Hospitalier Universitaire de Nice, C3M, Université Côte d’Azur, 06000 Nice, France
| | - Philippe Gual
- Team 8 “Chronic Liver Diseases Associated with Obesity and Alcohol”, INSERM, U1065, Centre Hospitalier Universitaire de Nice, C3M, Université Côte d’Azur, 06000 Nice, France
| | - Carmelo García-Monzón
- CIBERehd, ISCIII, 28029 Madrid, Spain
- Liver Research Unit, Santa Cristina University Hospital, Instituto de Investigación Sanitaria Princesa, 28009 Madrid, Spain
| | - Joan Caballería
- CIBERehd, ISCIII, 28029 Madrid, Spain
- Liver Unit, Hospital Clinic, 08036 Barcelona, Spain
| | - Azucena Castro
- OWL Metabolomics, Parque Tecnologico de Bizkaia, Building 502, 48160 Derio, Spain
| | - María Luz Martínez-Chantar
- CIC bioGUNE, Parque Tecnologico de Bizkaia, Building 801-A, 48160 Derio, Spain
- CIBERehd, ISCIII, 28029 Madrid, Spain
| | - José M. Mato
- CIC bioGUNE, Parque Tecnologico de Bizkaia, Building 801-A, 48160 Derio, Spain
- CIBERehd, ISCIII, 28029 Madrid, Spain
| | - Huiping Zhu
- Department of Nutritional Sciences, Dell Paediatric Research Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Richard H. Finnell
- Department of Nutritional Sciences, Dell Paediatric Research Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ana M. Aransay
- CIC bioGUNE, Parque Tecnologico de Bizkaia, Building 801-A, 48160 Derio, Spain
- CIBERehd, ISCIII, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-944-061-325 or +34-946-572-524; Fax: +34-946-572-530
| |
Collapse
|
14
|
Ibañez-Perez J, Díaz-Nuñez M, Clos-García M, Lainz L, Iglesias M, Díez-Zapirain M, Rabanal A, Bárcena L, González M, Lozano JJ, Marigorta UM, González E, Royo F, Aransay AM, Subiran N, Matorras R, Falcón-Pérez JM. microRNA-based signatures obtained from endometrial fluid identify implantative endometrium. Hum Reprod 2022; 37:2375-2391. [PMID: 36029522 PMCID: PMC9527456 DOI: 10.1093/humrep/deac184] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 09/30/2021] [Revised: 08/02/2022] [Indexed: 12/12/2022] Open
Abstract
STUDY QUESTION Is it possible to use free and extracellular vesicle-associated microRNAs (miRNAs) from human endometrial fluid (EF) samples as non-invasive biomarkers for implantative endometrium? SUMMARY ANSWER The free and extracellular vesicle-associated miRNAs can be used to detect implantative endometrium in a non-invasive manner. WHAT IS KNOWN ALREADY miRNAs and extracellular vesicles (EVs) from EF have been described as mediators of the embryo–endometrium crosstalk. Therefore, the analysis of miRNA from this fluid could become a non-invasive technique for recognizing implantative endometrium. This analysis could potentially help improve the implantation rates in ART. STUDY DESIGN, SIZE, DURATION In this prospective study, we first optimized different protocols for EVs and miRNA analyses using the EF of a setup cohort (n = 72). Then, we examined differentially expressed miRNAs in the EF of women with successful embryo implantation (discovery cohort n = 15/validation cohort n = 30) in comparison with those for whom the implantation had failed (discovery cohort n = 15/validation cohort n = 30). Successful embryo implantation was considered when pregnancy was confirmed by vaginal ultrasound showing a gestational sac 4 weeks after embryo transfer (ET). PARTICIPANTS/MATERIALS, SETTING, METHODS The EF of the setup cohort was obtained before starting fertility treatment during the natural cycle, 16–21 days after the beginning of menstruation. For the discovery and validation cohorts, the EF was collected from women undergoing frozen ET on Day 5, and the samples were collected immediately before ET. In this study, we compared five different methods; two of them based on direct extraction of RNA and the other three with an EV enrichment step before the RNA extraction. Small RNA sequencing was performed to determine the most efficient method and find a predictive model differentiating between implantative and non-implantative endometrium. The models were confirmed using quantitative PCR in two sets of samples (discovery and validation cohorts) with different implantation outcomes. MAIN RESULTS AND THE ROLE OF CHANCE The protocols using EV enrichment detected more miRNAs than the methods based on direct RNA extraction. The two most efficient protocols (using polymer-based precipitation (PBP): PBP-M and PBP-N) were used to obtain two predictive models (based on three miRNAs) allowing us to distinguish between an implantative and non-implantative endometrium. The first Model 1 (PBP-M) (discovery: AUC = 0.93; P-value = 0.003; validation: AUC = 0.69; P-value = 0.019) used hsa-miR-200b-3p, hsa-miR-24-3p and hsa-miR-148b-3p. Model 2 (PBP-N) (discovery: AUC = 0.92; P-value = 0.0002; validation: AUC = 0.78; P-value = 0.0002) used hsa-miR-200b-3p, hsa-miR-24-3p and hsa-miR-99b-5p. Functional analysis of these miRNAs showed strong association with key implantation processes such as in utero embryonic development or transforming growth factor-beta signaling. LARGE SCALE DATA The FASTQ data are available in the GEO database (access number GSE178917). LIMITATIONS, REASONS FOR CAUTION One important factor to consider is the inherent variability among the women involved in the trial and among the transferred embryos. The embryos were pre-selected based on morphology, but neither genetic nor molecular studies were conducted, which would have improved the accuracy of our tests. In addition, a limitation in miRNA library construction is the low amount of input RNA. WIDER IMPLICATIONS OF THE FINDINGS We describe new non-invasive protocols to analyze miRNAs from small volumes of EF. These protocols could be implemented in clinical practice to assess the status of the endometrium before attempting ET. Such evaluation could help to avoid the loss of embryos transferred to a non-implantative endometrium. STUDY FUNDING/COMPETING INTEREST(S) J.I.-P. was supported by a predoctoral grant from the Basque Government (PRE_2017_0204). This study was partially funded by the Grant for Fertility Innovation (GFI, 2011) from Merck (Darmstadt, Germany). It was also supported by the Spanish Ministry of Economy and Competitiveness MINECO within the National Plan RTI2018-094969-B-I00, the European Union's Horizon 2020 research and innovation program (860303), the Severo Ochoa Centre of Excellence Innovative Research Grant (SEV-2016-0644) and the Instituto de Salud Carlos III (PI20/01131). The funding entities did not play any role in the study design, collection, analysis and interpretation of data, writing of the report or the decision to submit the article for publication. The authors declare no competing interests.
Collapse
Affiliation(s)
- Jone Ibañez-Perez
- Human Reproduction Unit, Cruces University Hospital, University of the Basque Country (UPV/EHU), Barakaldo, Spain.,Innovation in Assisted Reproduction Group, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain.,Department of Obstetrics and Gynecology, University of the Basque Country (UPV/EHU), Leioa, Spain.,Exosomes Laboratory, CIC bioGUNE-BRTA, Derio, Spain
| | - María Díaz-Nuñez
- Human Reproduction Unit, Cruces University Hospital, University of the Basque Country (UPV/EHU), Barakaldo, Spain.,Innovation in Assisted Reproduction Group, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain
| | - Marc Clos-García
- Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lucía Lainz
- Human Reproduction Unit, Cruces University Hospital, University of the Basque Country (UPV/EHU), Barakaldo, Spain.,Innovation in Assisted Reproduction Group, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain
| | - María Iglesias
- Human Reproduction Unit, Cruces University Hospital, University of the Basque Country (UPV/EHU), Barakaldo, Spain.,Innovation in Assisted Reproduction Group, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain
| | - Miren Díez-Zapirain
- Human Reproduction Unit, Cruces University Hospital, University of the Basque Country (UPV/EHU), Barakaldo, Spain.,Innovation in Assisted Reproduction Group, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain
| | - Aintzane Rabanal
- Human Reproduction Unit, Cruces University Hospital, University of the Basque Country (UPV/EHU), Barakaldo, Spain.,Innovation in Assisted Reproduction Group, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain
| | - Laura Bárcena
- Genome Analysis Platform, CIC bioGUNE-BRTA, Derio, Spain
| | | | - Juan J Lozano
- Bioinformatics Platform, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Urko M Marigorta
- Integrative Genomics Lab, CIC bioGUNE-BRTA, Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | | | - Félix Royo
- Exosomes Laboratory, CIC bioGUNE-BRTA, Derio, Spain.,Centro de Investigación Biomédica en Red en el Área temática de Enfermedades Hepáticas (CIBEReh), Madrid, Spain
| | - Ana M Aransay
- Genome Analysis Platform, CIC bioGUNE-BRTA, Derio, Spain.,Centro de Investigación Biomédica en Red en el Área temática de Enfermedades Hepáticas (CIBEReh), Madrid, Spain
| | - Nerea Subiran
- Innovation in Assisted Reproduction Group, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain.,Department of Physiology, Faculty of Medicine and Dentistry, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Roberto Matorras
- Human Reproduction Unit, Cruces University Hospital, University of the Basque Country (UPV/EHU), Barakaldo, Spain.,Innovation in Assisted Reproduction Group, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain.,Department of Obstetrics and Gynecology, University of the Basque Country (UPV/EHU), Leioa, Spain.,Instituto Valenciano de Infertilidad (IVI) Bilbao/IVIRMA, Leioa, Spain
| | - Juan Manuel Falcón-Pérez
- Exosomes Laboratory, CIC bioGUNE-BRTA, Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.,Centro de Investigación Biomédica en Red en el Área temática de Enfermedades Hepáticas (CIBEReh), Madrid, Spain.,Metabolomics Platform, CIC bioGUNE-BRTA, Derio, Spain
| |
Collapse
|
15
|
Lario S, Ramírez-Lázaro MJ, Brunet-Vega A, Vila-Casadesús M, Aransay AM, Lozano JJ, Calvet X. Coding and non-coding co-expression network analysis identifies key modules and driver genes associated with precursor lesions of gastric cancer. Genomics 2022; 114:110370. [PMID: 35430283 DOI: 10.1016/j.ygeno.2022.110370] [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: 01/17/2022] [Revised: 03/23/2022] [Accepted: 04/11/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND Helicobacter pylori infection is the most important risk factor for gastric cancer (GC). Human gastric adenocarcinoma develops after long-term H. pylori infection via the Correa cascade. This carcinogenic pathway describes the progression from gastritis to atrophy, intestinal metaplasia (IM), dysplasia and GC. Patients with atrophy and intestinal metaplasia are considered to have precancerous lesions of GC (PLGC). H. pylori eradication and endoscopy surveillance are currently the only interventions for preventing GC. Better knowledge of the biology of human PLGC may help find stratification markers and contribute to better understanding of biological mechanisms. One way to achieve this is by using co-expression network analysis. Weighted gene co-expression network analysis (WGCNA) is often used to identify modules from co-expression networks and relate them to clinical traits. It also allows identification of driver genes that may be critical for PLGC. AIM The purpose of this study was to identify co-expression modules and differential gene expression in dyspeptic patients at different stages of the Correa pathway. METHODS We studied 96 gastric biopsies from 78 patients that were clinically classified as: non-active (n = 10) and chronic-active gastritis (n = 20), atrophy (n = 12), and IM (n = 36). Gene expression of coding RNAs was determined by microarrays and non-coding RNAs by RNA-seq. The WGCNA package was used for network construction, module detection, module preservation and hub and driver gene selection. RESULTS WGCNA identified 20 modules for coding RNAs and 4 for each miRNA and small RNA class. Modules were associated with antrum and corpus gastric locations, chronic gastritis and IM. Notably, coding RNA modules correlated with the Correa cascade. One was associated with the presence of H. pylori. In three modules, the module eigengene (ME) gradually increased in the stages toward IM, while in three others the inverse relationship was found. One miRNA module was negatively correlated to IM and was used for a mRNA-miRNA integration analysis. WGCNA also uncovered driver genes. Driver genes show both high connectivity within a module and are significantly associated with clinical traits. Some of those genes have been previously involved in H. pylori carcinogenesis, but others are new. Lastly, using similar external transcriptomic data, we confirmed that the discovered mRNA modules were highly preserved. CONCLUSION Our analysis captured co-expression modules that provide valuable information to understand the pathogenesis of the progression of PLGC.
Collapse
Affiliation(s)
- Sergio Lario
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain; Digestive Diseases Unit, Hospital Universitari Parc Taulí, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain.
| | - María J Ramírez-Lázaro
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain; Digestive Diseases Unit, Hospital Universitari Parc Taulí, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Anna Brunet-Vega
- Oncology Unit, Hospital Universitari Parc Taulí, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Maria Vila-Casadesús
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain; Bioinformatics Platform, CIBEREHD, Barcelona, Spain
| | - Ana M Aransay
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain; Genome Analysis Platform, CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, Spain
| | - Juan J Lozano
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain; Bioinformatics Platform, CIBEREHD, Barcelona, Spain
| | - Xavier Calvet
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain; Digestive Diseases Unit, Hospital Universitari Parc Taulí, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain; Departament de Medicina, UAB, Sabadell, Spain
| |
Collapse
|
16
|
Lozano-Ruiz B, Tzoumpa A, Martínez-Cardona C, Moreno D, Aransay AM, Cortazar AR, Picó J, Peiró G, Lozano J, Zapater P, Francés R, González-Navajas JM. Absent in Melanoma 2 (AIM2) Regulates the Stability of Regulatory T Cells. Int J Mol Sci 2022; 23:ijms23042230. [PMID: 35216346 PMCID: PMC8876789 DOI: 10.3390/ijms23042230] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 02/08/2022] [Accepted: 02/15/2022] [Indexed: 01/09/2023] Open
Abstract
Absent in melanoma 2 (AIM2) is a cytosolic dsDNA sensor that has been broadly studied for its role in inflammasome assembly. However, little is known about the function of AIM2 in adaptive immune cells. The purpose of this study was to investigate whether AIM2 has a cell-intrinsic role in CD4+ T cell differentiation or function. We found that AIM2 is expressed in both human and mouse CD4+ T cells and that its expression is affected by T cell receptor (TCR) activation. Naïve CD4+ T cells from AIM2-deficient (Aim2−/−) mice showed higher ability to maintain forkhead box P3 (FOXP3) expression in vitro, while their capacity to differentiate into T helper (Th)1, Th2 or Th17 cells remained unaltered. Transcriptional profiling by RNA sequencing showed that AIM2 might affect regulatory T cell (Treg) stability not by controlling the expression of Treg signature genes, but through the regulation of the cell’s metabolism. In addition, in a T cell transfer model of colitis, Aim2−/−-naïve T cells induced less severe body weight loss and displayed a higher ability to differentiate into FOXP3+ cells in vivo. In conclusion, we show that AIM2 function is not confined to innate immune cells but is also important in CD4+ T cells. Our data identify AIM2 as a regulator of FOXP3+ Treg cell differentiation and as a potential intervention target for restoring T cell homeostasis.
Collapse
Affiliation(s)
- Beatriz Lozano-Ruiz
- Alicante Institute for Health and Biomedical Research (ISABIAL), Hospital General Universitario Dr. Balmis, 03010 Alicante, Spain; (B.L.-R.); (A.T.); (C.M.-C.); (D.M.); (J.P.); (G.P.); (P.Z.); (R.F.)
| | - Amalia Tzoumpa
- Alicante Institute for Health and Biomedical Research (ISABIAL), Hospital General Universitario Dr. Balmis, 03010 Alicante, Spain; (B.L.-R.); (A.T.); (C.M.-C.); (D.M.); (J.P.); (G.P.); (P.Z.); (R.F.)
| | - Claudia Martínez-Cardona
- Alicante Institute for Health and Biomedical Research (ISABIAL), Hospital General Universitario Dr. Balmis, 03010 Alicante, Spain; (B.L.-R.); (A.T.); (C.M.-C.); (D.M.); (J.P.); (G.P.); (P.Z.); (R.F.)
| | - David Moreno
- Alicante Institute for Health and Biomedical Research (ISABIAL), Hospital General Universitario Dr. Balmis, 03010 Alicante, Spain; (B.L.-R.); (A.T.); (C.M.-C.); (D.M.); (J.P.); (G.P.); (P.Z.); (R.F.)
| | - Ana M. Aransay
- Networked Biomedical Research Center for Hepatic and Digestive Diseases (CIBERehd), Institute of Health Carlos III, 28029 Madrid, Spain; (A.M.A.); (J.L.)
- Center for Cooperative Research in Biosciences (CIC bioGUNE), 48160 Derio, Spain;
| | - Ana R. Cortazar
- Center for Cooperative Research in Biosciences (CIC bioGUNE), 48160 Derio, Spain;
| | - Joanna Picó
- Alicante Institute for Health and Biomedical Research (ISABIAL), Hospital General Universitario Dr. Balmis, 03010 Alicante, Spain; (B.L.-R.); (A.T.); (C.M.-C.); (D.M.); (J.P.); (G.P.); (P.Z.); (R.F.)
| | - Gloria Peiró
- Alicante Institute for Health and Biomedical Research (ISABIAL), Hospital General Universitario Dr. Balmis, 03010 Alicante, Spain; (B.L.-R.); (A.T.); (C.M.-C.); (D.M.); (J.P.); (G.P.); (P.Z.); (R.F.)
- Pathology Unit, Hospital General Universitario Dr. Balmis, 03010 Alicante, Spain
| | - Juanjo Lozano
- Networked Biomedical Research Center for Hepatic and Digestive Diseases (CIBERehd), Institute of Health Carlos III, 28029 Madrid, Spain; (A.M.A.); (J.L.)
| | - Pedro Zapater
- Alicante Institute for Health and Biomedical Research (ISABIAL), Hospital General Universitario Dr. Balmis, 03010 Alicante, Spain; (B.L.-R.); (A.T.); (C.M.-C.); (D.M.); (J.P.); (G.P.); (P.Z.); (R.F.)
- Networked Biomedical Research Center for Hepatic and Digestive Diseases (CIBERehd), Institute of Health Carlos III, 28029 Madrid, Spain; (A.M.A.); (J.L.)
- Department of Pharmacology, Pediatrics and Organic Chemistry, University Miguel Hernández (UMH), 03202 Elche, Spain
- Institute of Research, Development and Innovation in Healthcare Biotechnology in Elche (IDiBE), University Miguel Hernández (UMH), 03202 Elche, Spain
| | - Rubén Francés
- Alicante Institute for Health and Biomedical Research (ISABIAL), Hospital General Universitario Dr. Balmis, 03010 Alicante, Spain; (B.L.-R.); (A.T.); (C.M.-C.); (D.M.); (J.P.); (G.P.); (P.Z.); (R.F.)
- Networked Biomedical Research Center for Hepatic and Digestive Diseases (CIBERehd), Institute of Health Carlos III, 28029 Madrid, Spain; (A.M.A.); (J.L.)
- Institute of Research, Development and Innovation in Healthcare Biotechnology in Elche (IDiBE), University Miguel Hernández (UMH), 03202 Elche, Spain
- Department of Clinical Medicine, University Miguel Hernández (UMH), 03202 Elche, Spain
| | - José M. González-Navajas
- Alicante Institute for Health and Biomedical Research (ISABIAL), Hospital General Universitario Dr. Balmis, 03010 Alicante, Spain; (B.L.-R.); (A.T.); (C.M.-C.); (D.M.); (J.P.); (G.P.); (P.Z.); (R.F.)
- Networked Biomedical Research Center for Hepatic and Digestive Diseases (CIBERehd), Institute of Health Carlos III, 28029 Madrid, Spain; (A.M.A.); (J.L.)
- Department of Pharmacology, Pediatrics and Organic Chemistry, University Miguel Hernández (UMH), 03202 Elche, Spain
- Institute of Research, Development and Innovation in Healthcare Biotechnology in Elche (IDiBE), University Miguel Hernández (UMH), 03202 Elche, Spain
- Correspondence: ; Tel.: +34-965913928
| |
Collapse
|
17
|
Pellon A, Barriales D, Peña-Cearra A, Castelo-Careaga J, Palacios A, Lopez N, Atondo E, Pascual-Itoiz MA, Martín-Ruiz I, Sampedro L, Gonzalez-Lopez M, Bárcena L, Martín-Mateos T, Landete JM, Prados-Rosales R, Plaza-Vinuesa L, Muñoz R, de las Rivas B, Rodríguez JM, Berra E, Aransay AM, Abecia L, Lavín JL, Rodríguez H, Anguita J. The commensal bacterium Lactiplantibacillus plantarum imprints innate memory-like responses in mononuclear phagocytes. Gut Microbes 2022; 13:1939598. [PMID: 34224309 PMCID: PMC8259724 DOI: 10.1080/19490976.2021.1939598] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Gut microbiota is a constant source of antigens and stimuli to which the resident immune system has developed tolerance. However, the mechanisms by which mononuclear phagocytes, specifically monocytes/macrophages, cope with these usually pro-inflammatory signals are poorly understood. Here, we show that innate immune memory promotes anti-inflammatory homeostasis, using as model strains of the commensal bacterium Lactiplantibacillus plantarum. Priming of monocytes/macrophages with bacteria, especially in its live form, enhances bacterial intracellular survival and decreases the release of pro-inflammatory signals to the environment, with lower production of TNF and higher levels of IL-10. Analysis of the transcriptomic landscape of these cells shows downregulation of pathways associated with the production of reactive oxygen species (ROS) and the release of cytokines, chemokines and antimicrobial peptides. Indeed, the induction of ROS prevents memory-induced bacterial survival. In addition, there is a dysregulation in gene expression of several metabolic pathways leading to decreased glycolytic and respiratory rates in memory cells. These data support commensal microbe-specific metabolic changes in innate immune memory cells that might contribute to homeostasis in the gut.
Collapse
Affiliation(s)
- Aize Pellon
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
| | - Diego Barriales
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
| | - Ainize Peña-Cearra
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain,Faculty of Medicine and Nursing, Universidad Del Pais Vasco (UPV/EHU), Leioa, Spain
| | - Janire Castelo-Careaga
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
| | - Ainhoa Palacios
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
| | - Nerea Lopez
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
| | - Estibaliz Atondo
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
| | - Miguel Angel Pascual-Itoiz
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
| | - Itziar Martín-Ruiz
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
| | - Leticia Sampedro
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
| | | | - Laura Bárcena
- Genomic Analysis Platform, CIC bioGUNE-BRTA, Derio, Spain
| | - Teresa Martín-Mateos
- Physiopathology of the Hypoxia-signaling Pathway Laboratory, CIC bioGUNE-BRTA, Derio, Spain
| | - Jose María Landete
- Departamento De Tecnología De Alimentos, Instituto Nacional De Investigación Y Tecnología Agraria Y Alimentaria (INIA), Madrid, Spain
| | - Rafael Prados-Rosales
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain,Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, United Kingdom; RPR: Department of Preventive Medicine and Public Health and Microbiology, Universidad Autónoma De Madrid, Madrid 28029, Spain; JLL: Applied Mathematics Department, Bioinformatics Unit, NEIKER-BRTA, Parque Tecnológico De Bizkaia, Derio, Spain
| | - Laura Plaza-Vinuesa
- Laboratorio De Biotecnología Bacteriana, Instituto De Ciencia Y Tecnología De Alimentos Y Nutrición (ICTAN-CSIC), Madrid, Spain
| | - Rosario Muñoz
- Laboratorio De Biotecnología Bacteriana, Instituto De Ciencia Y Tecnología De Alimentos Y Nutrición (ICTAN-CSIC), Madrid, Spain
| | - Blanca de las Rivas
- Laboratorio De Biotecnología Bacteriana, Instituto De Ciencia Y Tecnología De Alimentos Y Nutrición (ICTAN-CSIC), Madrid, Spain
| | - Juan Miguel Rodríguez
- Department of Nutrition and Food Science, Universidad Complutense De Madrid, Madrid, Spain
| | - Edurne Berra
- Physiopathology of the Hypoxia-signaling Pathway Laboratory, CIC bioGUNE-BRTA, Derio, Spain
| | - Ana M. Aransay
- Genomic Analysis Platform, CIC bioGUNE-BRTA, Derio, Spain,CIBERehd, ISCIII, Madrid, Spain
| | - Leticia Abecia
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain,Faculty of Medicine and Nursing, Universidad Del Pais Vasco (UPV/EHU), Leioa, Spain
| | - Jose Luis Lavín
- Bioinformatics Unit, CIC bioGUNE-BRTA, Derio, Spain,Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, United Kingdom; RPR: Department of Preventive Medicine and Public Health and Microbiology, Universidad Autónoma De Madrid, Madrid 28029, Spain; JLL: Applied Mathematics Department, Bioinformatics Unit, NEIKER-BRTA, Parque Tecnológico De Bizkaia, Derio, Spain
| | - Hector Rodríguez
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain,Hector Rodríguez Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio48160, Spain
| | - Juan Anguita
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia, Spain,CONTACT Juan Anguita Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio48160, Spain
| |
Collapse
|
18
|
Zhang IW, Curto A, López-Vicario C, Casulleras M, Duran-Güell M, Flores-Costa R, Colsch B, Aguilar F, Aransay AM, Lozano JJ, Hernández-Tejero M, Toapanta D, Fernández J, Arroyo V, Clària J. Mitochondrial dysfunction governs immunometabolism in leukocytes of patients with acute-on-chronic liver failure. J Hepatol 2022; 76:93-106. [PMID: 34450236 DOI: 10.1016/j.jhep.2021.08.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [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: 12/22/2020] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND & AIMS Patients with acute-on-chronic liver failure (ACLF) present a systemic hyperinflammatory response associated with increased circulating levels of small-molecule metabolites. To investigate whether these alterations reflect inadequate cell energy output, we assessed mitochondrial morphology and central metabolic pathways with emphasis on the tricarboxylic acid (TCA) cycle in peripheral leukocytes from patients with acutely decompensated (AD) cirrhosis, with and without ACLF. METHODS The study included samples from patients with AD cirrhosis (108 without and 128 with ACLF) and 41 healthy individuals. Leukocyte mitochondrial ultrastructure was visualized by transmission electron microscopy and cytosolic and mitochondrial metabolic fluxes were determined by assessing NADH/FADH2 production from various substrates. Plasma GDF15 and FGF21 were determined by Luminex and acylcarnitines by LC-MS/MS. Gene expression was analyzed by RNA-sequencing and PCR-based glucose metabolism profiler array. RESULTS Mitochondrial ultrastructure in patients with advanced cirrhosis was distinguished by cristae rarefication and swelling. The number of mitochondria per leukocyte was higher in patients, accompanied by a reduction in their size. Increased FGF21 and C6:0- and C8:0-carnitine predicted mortality whereas GDF15 strongly correlated with a gene set signature related to leukocyte activation. Metabolic flux analyses revealed increased energy production in mononuclear leukocytes from patients with preferential involvement of extra-mitochondrial pathways, supported by upregulated expression of genes encoding enzymes of the glycolytic and pentose phosphate pathways. In patients with ACLF, mitochondrial function analysis uncovered break-points in the TCA cycle at the isocitrate dehydrogenase and succinate dehydrogenase level, which were bridged by anaplerotic reactions involving glutaminolysis and nucleoside metabolism. CONCLUSIONS Our findings provide evidence at the cellular, organelle and biochemical levels that severe mitochondrial dysfunction governs immunometabolism in leukocytes from patients with AD cirrhosis and ACLF. LAY SUMMARY Patients at advanced stages of liver disease have dismal prognosis due to vital organ failures and the lack of treatment options. In this study, we report that the functioning of mitochondria, which are known as the cell powerhouse, is severely impaired in leukocytes of these patients, probably as a consequence of intense inflammation. Mitochondrial dysfunction is therefore a hallmark of advanced liver disease.
Collapse
Affiliation(s)
- Ingrid W Zhang
- Biochemistry and Molecular Genetics Service, Hospital Clínic-IDIBAPS, Barcelona, Spain; European Foundation for the Study of Chronic Liver Failure (EF Clif) and Grifols Chair, Barcelona, Spain
| | - Anna Curto
- European Foundation for the Study of Chronic Liver Failure (EF Clif) and Grifols Chair, Barcelona, Spain
| | - Cristina López-Vicario
- Biochemistry and Molecular Genetics Service, Hospital Clínic-IDIBAPS, Barcelona, Spain; European Foundation for the Study of Chronic Liver Failure (EF Clif) and Grifols Chair, Barcelona, Spain
| | - Mireia Casulleras
- Biochemistry and Molecular Genetics Service, Hospital Clínic-IDIBAPS, Barcelona, Spain; European Foundation for the Study of Chronic Liver Failure (EF Clif) and Grifols Chair, Barcelona, Spain
| | - Marta Duran-Güell
- Biochemistry and Molecular Genetics Service, Hospital Clínic-IDIBAPS, Barcelona, Spain; European Foundation for the Study of Chronic Liver Failure (EF Clif) and Grifols Chair, Barcelona, Spain
| | - Roger Flores-Costa
- Biochemistry and Molecular Genetics Service, Hospital Clínic-IDIBAPS, Barcelona, Spain; European Foundation for the Study of Chronic Liver Failure (EF Clif) and Grifols Chair, Barcelona, Spain
| | - Benoit Colsch
- Laboratoire d'Etude du Metabolisme des Medicaments, CEA, INRA, Universite Paris Saclay, MetaboHUB, F-91191 Gif-sur-Yvette, France
| | - Ferran Aguilar
- European Foundation for the Study of Chronic Liver Failure (EF Clif) and Grifols Chair, Barcelona, Spain
| | - Ana M Aransay
- CIC bioGUNE, Parque Tecnológico de Bizkaia, Derio, Bizkaia, Spain; CIBERehd, Barcelona, Spain
| | | | | | - David Toapanta
- Liver ICU, Liver Unit, Hospital Clínic-IDIBAPS, Barcelona, Spain
| | - Javier Fernández
- European Foundation for the Study of Chronic Liver Failure (EF Clif) and Grifols Chair, Barcelona, Spain; CIBERehd, Barcelona, Spain; Liver ICU, Liver Unit, Hospital Clínic-IDIBAPS, Barcelona, Spain
| | - Vicente Arroyo
- European Foundation for the Study of Chronic Liver Failure (EF Clif) and Grifols Chair, Barcelona, Spain
| | - Joan Clària
- Biochemistry and Molecular Genetics Service, Hospital Clínic-IDIBAPS, Barcelona, Spain; European Foundation for the Study of Chronic Liver Failure (EF Clif) and Grifols Chair, Barcelona, Spain; CIBERehd, Barcelona, Spain; Department of Biomedical Sciences, University of Barcelona, Barcelona, Spain.
| |
Collapse
|
19
|
Barroso-Gomila O, Trulsson F, Muratore V, Canosa I, Merino-Cacho L, Cortazar AR, Pérez C, Azkargorta M, Iloro I, Carracedo A, Aransay AM, Elortza F, Mayor U, Vertegaal ACO, Barrio R, Sutherland JD. Identification of proximal SUMO-dependent interactors using SUMO-ID. Nat Commun 2021; 12:6671. [PMID: 34795231 PMCID: PMC8602451 DOI: 10.1038/s41467-021-26807-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 10/19/2021] [Indexed: 12/13/2022] Open
Abstract
The fast dynamics and reversibility of posttranslational modifications by the ubiquitin family pose significant challenges for research. Here we present SUMO-ID, a technology that merges proximity biotinylation by TurboID and protein-fragment complementation to find SUMO-dependent interactors of proteins of interest. We develop an optimized split-TurboID version and show SUMO interaction-dependent labelling of proteins proximal to PML and RANGAP1. SUMO-dependent interactors of PML are involved in transcription, DNA damage, stress response and SUMO modification and are highly enriched in SUMO Interacting Motifs, but may only represent a subset of the total PML proximal proteome. Likewise, SUMO-ID also allow us to identify interactors of SUMOylated SALL1, a less characterized SUMO substrate. Furthermore, using TP53 as a substrate, we identify SUMO1, SUMO2 and Ubiquitin preferential interactors. Thus, SUMO-ID is a powerful tool that allows to study the consequences of SUMO-dependent interactions, and may further unravel the complexity of the ubiquitin code.
Collapse
Affiliation(s)
- Orhi Barroso-Gomila
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain
| | - Fredrik Trulsson
- grid.10419.3d0000000089452978Cell and Chemical Biology, Leiden University Medical Center (LUMC), 2333 ZA Leiden, The Netherlands
| | - Veronica Muratore
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain
| | - Iñigo Canosa
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain
| | - Laura Merino-Cacho
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain
| | - Ana Rosa Cortazar
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain ,grid.413448.e0000 0000 9314 1427CIBERONC, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain
| | - Coralia Pérez
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain
| | - Mikel Azkargorta
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain ,grid.413448.e0000 0000 9314 1427CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain ,grid.413448.e0000 0000 9314 1427ProteoRed-ISCIII, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain
| | - Ibon Iloro
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain ,grid.413448.e0000 0000 9314 1427CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain ,grid.413448.e0000 0000 9314 1427ProteoRed-ISCIII, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain
| | - Arkaitz Carracedo
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain ,grid.413448.e0000 0000 9314 1427CIBERONC, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain ,grid.424810.b0000 0004 0467 2314Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain ,grid.11480.3c0000000121671098Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), E-48940 Leioa, Spain
| | - Ana M. Aransay
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain ,grid.413448.e0000 0000 9314 1427CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain
| | - Felix Elortza
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain ,grid.413448.e0000 0000 9314 1427CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain ,grid.413448.e0000 0000 9314 1427ProteoRed-ISCIII, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain
| | - Ugo Mayor
- grid.424810.b0000 0004 0467 2314Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain ,grid.11480.3c0000000121671098Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), E-48940 Leioa, Spain
| | - Alfred C. O. Vertegaal
- grid.10419.3d0000000089452978Cell and Chemical Biology, Leiden University Medical Center (LUMC), 2333 ZA Leiden, The Netherlands
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160, Derio, Spain.
| | - James D. Sutherland
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801 A, 48160 Derio, Spain
| |
Collapse
|
20
|
Giordano I, Pirone L, Muratore V, Landaluze E, Pérez C, Lang V, Garde-Lapido E, Gonzalez-Lopez M, Barroso-Gomila O, Vertegaal ACO, Aransay AM, Rodriguez JA, Rodriguez MS, Sutherland JD, Barrio R. SALL1 Modulates CBX4 Stability, Nuclear Bodies, and Regulation of Target Genes. Front Cell Dev Biol 2021; 9:715868. [PMID: 34621739 PMCID: PMC8490708 DOI: 10.3389/fcell.2021.715868] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
Development is orchestrated through a complex interplay of multiple transcription factors. The comprehension of this interplay will help us to understand developmental processes. Here we analyze the relationship between two key transcription factors: CBX4, a member of the Polycomb Repressive Complex 1 (PRC1), and SALL1, a member of the Spalt-like family with important roles in embryogenesis and limb development. Both proteins localize to nuclear bodies and are modified by the small ubiquitin-like modifier (SUMO). Our results show that CBX4 and SALL1 interact in the nucleoplasm and that increased SALL1 expression reduces ubiquitination of CBX4, enhancing its stability. This is accompanied by an increase in the number and size of CBX4-containing Polycomb bodies, and by a greater repression of CBX4 target genes. Thus, our findings uncover a new way of SALL1-mediated regulation of Polycomb bodies through modulation of CBX4 stability, with consequences in the regulation of its target genes, which could have an impact in cell differentiation and development.
Collapse
Affiliation(s)
- Immacolata Giordano
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Lucia Pirone
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Veronica Muratore
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Eukene Landaluze
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Coralia Pérez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Valerie Lang
- Viralgen Vector Core, Parque Científico y Tecnológico de Guipúzcoa, San Sebastián, Spain
| | - Elisa Garde-Lapido
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Monika Gonzalez-Lopez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Orhi Barroso-Gomila
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Ana M Aransay
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain.,Centro de Investigación Biomédica en Red. Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose Antonio Rodriguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Spain
| | - Manuel S Rodriguez
- Laboratoire de Chimie de Coordination-CNRS, Paul Sabatier: Université Toulouse III, Toulouse, France
| | - James D Sutherland
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain
| |
Collapse
|
21
|
Rodriguez RM, Hernández-Fuentes MP, Corte-Iglesias V, Saiz ML, Lozano JJ, Cortazar AR, Mendizabal I, Suarez-Fernandez ML, Coto E, López-Vázquez A, Díaz-Corte C, Aransay AM, López-Larrea C, Suarez-Álvarez B. Defining a Methylation Signature Associated With Operational Tolerance in Kidney Transplant Recipients. Front Immunol 2021; 12:709164. [PMID: 34489960 PMCID: PMC8417883 DOI: 10.3389/fimmu.2021.709164] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/03/2021] [Indexed: 12/27/2022] Open
Abstract
Operational tolerance after kidney transplantation is defined as stable graft acceptance without the need for immunosuppression therapy. However, it is not clear which cellular and molecular pathways are driving tolerance in these patients. We performed genome-wide analysis of DNA methylation in peripheral blood mononuclear cells from kidney transplant recipients with chronic rejection and operational tolerance from the Genetic Analysis of Molecular Biomarkers of Immunological Tolerance (GAMBIT) study. Our results showed that both clinical stages diverge in 2737 genes, indicating that each one has a specific methylation signature associated with transplant outcome. We also observed that tolerance is associated with demethylation in genes involved in immune function, including B and T cell activation and Th17 differentiation, while in chronic rejection it is associated with intracellular signaling and ubiquitination pathways. Using co-expression network analysis, we selected 12 genomic regions that are specifically hypomethylated or hypermethylated in tolerant patients. Analysis of these genes in transplanted patients with low dose of steroids showed that these have a similar methylation signature to that of tolerant recipients. Overall, these results demonstrate that methylation analysis can mirror the immune status associated with transplant outcome and provides a starting point for understanding the epigenetic mechanisms associated with tolerance.
Collapse
Affiliation(s)
- Ramon M Rodriguez
- Translation Immunology Laboratory, Instituto de Investigación Sanitaria del Principado de Asturias-ISPA, Oviedo, Spain.,Red de Investigación Renal (REDinREN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Lipids in Human Pathology, Institut d'Investigació Sanitària Illes Balears (IdISBa, Health Research Institute of the Balearic Islands), Palma, Spain
| | - María P Hernández-Fuentes
- MRC Centre for Transplantation, King's Health Partners, Guy's Hospital, King's College London, London, United Kingdom
| | - Viviana Corte-Iglesias
- Translation Immunology Laboratory, Instituto de Investigación Sanitaria del Principado de Asturias-ISPA, Oviedo, Spain
| | - María Laura Saiz
- Translation Immunology Laboratory, Instituto de Investigación Sanitaria del Principado de Asturias-ISPA, Oviedo, Spain
| | - Juan José Lozano
- Bioinformatics Platform, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Ana R Cortazar
- Genome Analysis Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Derio, Spain
| | - Isabel Mendizabal
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | | | - Eliecer Coto
- Red de Investigación Renal (REDinREN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain
| | - Antonio López-Vázquez
- Translation Immunology Laboratory, Instituto de Investigación Sanitaria del Principado de Asturias-ISPA, Oviedo, Spain.,Red de Investigación Renal (REDinREN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Immunology Department, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Carmen Díaz-Corte
- Red de Investigación Renal (REDinREN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Nephrology Department, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Ana M Aransay
- Genome Analysis Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Derio, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Carlos López-Larrea
- Translation Immunology Laboratory, Instituto de Investigación Sanitaria del Principado de Asturias-ISPA, Oviedo, Spain.,Red de Investigación Renal (REDinREN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Immunology Department, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Beatriz Suarez-Álvarez
- Translation Immunology Laboratory, Instituto de Investigación Sanitaria del Principado de Asturias-ISPA, Oviedo, Spain.,Red de Investigación Renal (REDinREN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| |
Collapse
|
22
|
Palomo-Irigoyen M, Pérez-Andrés E, Iruarrizaga-Lejarreta M, Barreira-Manrique A, Tamayo-Caro M, Vila-Vecilla L, Moreno-Cugnon L, Beitia N, Medrano D, Fernández-Ramos D, Lozano JJ, Okawa S, Lavín JL, Martín-Martín N, Sutherland JD, de Juan VG, Gonzalez-Lopez M, Macías-Cámara N, Mosén-Ansorena D, Laraba L, Hanemann CO, Ercolano E, Parkinson DB, Schultz CW, Araúzo-Bravo MJ, Ascensión AM, Gerovska D, Iribar H, Izeta A, Pytel P, Krastel P, Provenzani A, Seneci P, Carrasco RD, Del Sol A, Martinez-Chantar ML, Barrio R, Serra E, Lazaro C, Flanagan AM, Gorospe M, Ratner N, Aransay AM, Carracedo A, Varela-Rey M, Woodhoo A. HuR/ELAVL1 drives malignant peripheral nerve sheath tumor growth and metastasis. J Clin Invest 2021; 130:3848-3864. [PMID: 32315290 PMCID: PMC7324187 DOI: 10.1172/jci130379] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 04/14/2020] [Indexed: 12/28/2022] Open
Abstract
Cancer cells can develop a strong addiction to discrete molecular regulators, which control the aberrant gene expression programs that drive and maintain the cancer phenotype. Here, we report the identification of the RNA-binding protein HuR/ELAVL1 as a central oncogenic driver for malignant peripheral nerve sheath tumors (MPNSTs), which are highly aggressive sarcomas that originate from cells of the Schwann cell lineage. HuR was found to be highly elevated and bound to a multitude of cancer-associated transcripts in human MPNST samples. Accordingly, genetic and pharmacological inhibition of HuR had potent cytostatic and cytotoxic effects on tumor growth, and strongly suppressed metastatic capacity in vivo. Importantly, we linked the profound tumorigenic function of HuR to its ability to simultaneously regulate multiple essential oncogenic pathways in MPNST cells, including the Wnt/β-catenin, YAP/TAZ, RB/E2F, and BET pathways, which converge on key transcriptional networks. Given the exceptional dependency of MPNST cells on HuR for survival, proliferation, and dissemination, we propose that HuR represents a promising therapeutic target for MPNST treatment.
Collapse
Affiliation(s)
- Marta Palomo-Irigoyen
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Encarni Pérez-Andrés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Marta Iruarrizaga-Lejarreta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Adrián Barreira-Manrique
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Miguel Tamayo-Caro
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Laura Vila-Vecilla
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Leire Moreno-Cugnon
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Nagore Beitia
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Daniela Medrano
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - David Fernández-Ramos
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan José Lozano
- Bioinformatic Platform, CIBERehd, Instituto de Salud Carlos III, Barcelona, Spain
| | - Satoshi Okawa
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg.,Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | - José L Lavín
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Natalia Martín-Martín
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - James D Sutherland
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Virginia Guitiérez de Juan
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Monika Gonzalez-Lopez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Nuria Macías-Cámara
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - David Mosén-Ansorena
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Liyam Laraba
- Institute of Translational and Stratified Medicine, Faculty of Medicine and Dentistry, Plymouth University, Derriford Research Facility, Devon, United Kingdom
| | - C Oliver Hanemann
- Institute of Translational and Stratified Medicine, Faculty of Medicine and Dentistry, Plymouth University, Derriford Research Facility, Devon, United Kingdom
| | - Emanuela Ercolano
- Institute of Translational and Stratified Medicine, Faculty of Medicine and Dentistry, Plymouth University, Derriford Research Facility, Devon, United Kingdom
| | - David B Parkinson
- Institute of Translational and Stratified Medicine, Faculty of Medicine and Dentistry, Plymouth University, Derriford Research Facility, Devon, United Kingdom
| | | | - Marcos J Araúzo-Bravo
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebastián, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Alex M Ascensión
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebastián, Spain
| | - Daniela Gerovska
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebastián, Spain
| | - Haizea Iribar
- Tissue Engineering Laboratory, Bioengineering Area, Instituto Biodonostia, San Sebastián, Spain
| | - Ander Izeta
- Tissue Engineering Laboratory, Bioengineering Area, Instituto Biodonostia, San Sebastián, Spain
| | - Peter Pytel
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
| | - Philipp Krastel
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Alessandro Provenzani
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | - Ruben D Carrasco
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Antonio Del Sol
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain.,Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - María Luz Martinez-Chantar
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Eduard Serra
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain.,Hereditary Cancer Group, Institute for Health Science Research Germans Trias I Pujol (IGTP) and Program of Predictive and Personalized Medicine of Cancer (PMPPC), Barcelona, Spain
| | - Conxi Lazaro
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology, and.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Adrienne M Flanagan
- Department of Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, United Kingdom.,UCL Cancer Institute, University College London, London, United Kingdom
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, Maryland, USA
| | - Nancy Ratner
- Division of Experimental Hematology and Cancer Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, USA
| | - Ana M Aransay
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Arkaitz Carracedo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.,Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Marta Varela-Rey
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Ashwin Woodhoo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| |
Collapse
|
23
|
Royo F, Azkargorta M, Lavin JL, Clos-Garcia M, Cortazar AR, Gonzalez-Lopez M, Barcena L, Del Portillo HA, Yáñez-Mó M, Marcilla A, Borras FE, Peinado H, Guerrero I, Váles-Gómez M, Cereijo U, Sardon T, Aransay AM, Elortza F, Falcon-Perez JM. Extracellular Vesicles From Liver Progenitor Cells Downregulates Fibroblast Metabolic Activity and Increase the Expression of Immune-Response Related Molecules. Front Cell Dev Biol 2021; 8:613583. [PMID: 33511119 PMCID: PMC7835421 DOI: 10.3389/fcell.2020.613583] [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: 10/02/2020] [Accepted: 12/07/2020] [Indexed: 11/25/2022] Open
Abstract
Extracellular vesicles (EVs) mediate cell-to-cell crosstalk whose content can induce changes in acceptor cells and their microenvironment. MLP29 cells are mouse liver progenitor cells that release EVs loaded with signaling cues that could affect cell fate. In the current work, we incubated 3T3-L1 mouse fibroblasts with MLP29-derived EVs, and then analyzed changes by proteomics and transcriptomics. Results showed a general downregulation of protein and transcript expression related to proliferative and metabolic routes dependent on TGF-beta. We also observed an increase in the ERBB2 interacting protein (ERBIN) and Cxcl2, together with an induction of ribosome biogenesis and interferon-related response molecules, suggesting the activation of immune system signaling.
Collapse
Affiliation(s)
- Felix Royo
- Center for Cooperative Research in Biosciences, Bizkaia Technology Park, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
| | - Mikel Azkargorta
- Center for Cooperative Research in Biosciences, Bizkaia Technology Park, Bizkaia, Spain
| | - Jose L Lavin
- Center for Cooperative Research in Biosciences, Bizkaia Technology Park, Bizkaia, Spain
| | - Marc Clos-Garcia
- Center for Cooperative Research in Biosciences, Bizkaia Technology Park, Bizkaia, Spain
| | - Ana R Cortazar
- Center for Cooperative Research in Biosciences, Bizkaia Technology Park, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Instituto de Salud Carlos III, Madrid, Spain
| | - Monika Gonzalez-Lopez
- Center for Cooperative Research in Biosciences, Bizkaia Technology Park, Bizkaia, Spain
| | - Laura Barcena
- Center for Cooperative Research in Biosciences, Bizkaia Technology Park, Bizkaia, Spain
| | - Hernando A Del Portillo
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Health Sciences Research Institute Germans Trias i Pujol, Badalona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - María Yáñez-Mó
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa, Instituto de Investigaciones Sanitarias la Princesa, Universidad Autónoma de Madrid, Madrid, Spain
| | - Antonio Marcilla
- Àrea de Parasitologia, Departament de Farmàcia i Tecnologia Farmacèutica i Parasitologia, Universitat de València, Valencia, Spain.,Joint Research Unit on Endocrinology, Nutrition and Clinical Dietetics, Health Research Institute La Fe, Universitat de València, Valencia, Spain
| | - Francesc E Borras
- Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona, Barcelona, Spain.,REMAR-IVECAT Group-"Germans Trias i Pujol" Health Science Research Institute (IGTP), Badalona, Spain.,Nephrology Department-"Germans Trias i Pujol" University Hospital, Can Ruti Campus, Badalona, Spain
| | - Hector Peinado
- Microenvironment and Metastasis Laboratory, Molecular Oncology Program, Spanish National Cancer Research Center, Madrid, Spain
| | - Isabel Guerrero
- Tissue and Organ Homeostasis, Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Madrid, Spain
| | - Mar Váles-Gómez
- Spanish National Centre for Biotechnology, Spanish National Research Council, Madrid, Spain
| | | | | | - Ana M Aransay
- Center for Cooperative Research in Biosciences, Bizkaia Technology Park, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
| | - Felix Elortza
- Center for Cooperative Research in Biosciences, Bizkaia Technology Park, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
| | - Juan M Falcon-Perez
- Center for Cooperative Research in Biosciences, Bizkaia Technology Park, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| |
Collapse
|
24
|
Barriales D, Martín-Ruiz I, Carreras-González A, Montesinos-Robledo M, Azkargorta M, Iloro I, Escobés I, Martín-Mateos T, Atondo E, Palacios A, Gonzalez-Lopez M, Bárcena L, Cortázar AR, Cabrera D, Peña-Cearra A, van Liempd SM, Falcón-Pérez JM, Pascual-Itoiz MA, Flores JM, Abecia L, Pellon A, Martínez-Chantar ML, Aransay AM, Pascual A, Elortza F, Berra E, Lavín JL, Rodríguez H, Anguita J. Borrelia burgdorferi infection induces long-term memory-like responses in macrophages with tissue-wide consequences in the heart. PLoS Biol 2021; 19:e3001062. [PMID: 33395408 PMCID: PMC7808612 DOI: 10.1371/journal.pbio.3001062] [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] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 01/14/2021] [Accepted: 12/22/2020] [Indexed: 11/19/2022] Open
Abstract
Lyme carditis is an extracutaneous manifestation of Lyme disease characterized by episodes of atrioventricular block of varying degrees and additional, less reported cardiomyopathies. The molecular changes associated with the response to Borrelia burgdorferi over the course of infection are poorly understood. Here, we identify broad transcriptomic and proteomic changes in the heart during infection that reveal a profound down-regulation of mitochondrial components. We also describe the long-term functional modulation of macrophages exposed to live bacteria, characterized by an augmented glycolytic output, increased spirochetal binding and internalization, and reduced inflammatory responses. In vitro, glycolysis inhibition reduces the production of tumor necrosis factor (TNF) by memory macrophages, whereas in vivo, it produces the reversion of the memory phenotype, the recovery of tissue mitochondrial components, and decreased inflammation and spirochetal burdens. These results show that B. burgdorferi induces long-term, memory-like responses in macrophages with tissue-wide consequences that are amenable to be manipulated in vivo. Lyme carditis is a manifestation of Lyme disease characterized by episodes of atrioventricular block and additional cardiomyopathies. This study describes the proteomic and transcriptomic changes in the heart upon infection with Borrelia burgdorferi, and identifies innate immune memory hallmarks specific to the response to the spirochete that are amenable to therapeutic manipulation.
Collapse
Affiliation(s)
- Diego Barriales
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
| | - Itziar Martín-Ruiz
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
| | - Ana Carreras-González
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
| | - Marta Montesinos-Robledo
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
| | - Mikel Azkargorta
- Proteomics Platform, ProteoRed-ISCIII, CIC bioGUNE-BRTA, Derio, Spain
| | - Ibon Iloro
- Proteomics Platform, ProteoRed-ISCIII, CIC bioGUNE-BRTA, Derio, Spain
| | - Iraide Escobés
- Proteomics Platform, ProteoRed-ISCIII, CIC bioGUNE-BRTA, Derio, Spain
| | - Teresa Martín-Mateos
- Physiopathology of the Hypoxia-Signaling Pathway Laboratory, CIC bioGUNE-BRTA, Derio, Spain
| | - Estibaliz Atondo
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
| | - Ainhoa Palacios
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
| | | | - Laura Bárcena
- Genomic Analysis Platform, CIC bioGUNE-BRTA, Derio, Spain
| | | | - Diana Cabrera
- Metabolomics Platform, CIC bioGUNE-BRTA, Derio, Spain
| | - Ainize Peña-Cearra
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
| | | | - Juan M. Falcón-Pérez
- Metabolomics Platform, CIC bioGUNE-BRTA, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Miguel A. Pascual-Itoiz
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
| | - Juana María Flores
- Department of Animal Medicine and Surgery, Veterinary Faculty, Universidad Complutense de Madrid, Madrid, Spain
| | - Leticia Abecia
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
| | - Aize Pellon
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
| | | | - Ana M. Aransay
- Genomic Analysis Platform, CIC bioGUNE-BRTA, Derio, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Alberto Pascual
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Felix Elortza
- Proteomics Platform, ProteoRed-ISCIII, CIC bioGUNE-BRTA, Derio, Spain
| | - Edurne Berra
- Physiopathology of the Hypoxia-Signaling Pathway Laboratory, CIC bioGUNE-BRTA, Derio, Spain
| | | | - Héctor Rodríguez
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
| | - Juan Anguita
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- * E-mail:
| |
Collapse
|
25
|
Inglés-Ferrándiz M, Martin-Inaraja M, Herrera L, Villaverde M, Santos S, Vesga MA, Garreta E, Martín-Ruiz I, Aransay AM, Anguita J, Barreña B, Allende LM, Gonzalez-Granado LI, Eguizabal C. Generation, establishment and characterization of a pluripotent stem cell line (CVTTHi001-A) from primary fibroblasts isolated from a patient with activated PI3 kinase delta syndrome (APDS2). Stem Cell Res 2020; 49:102082. [PMID: 33221676 DOI: 10.1016/j.scr.2020.102082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 11/01/2020] [Indexed: 11/27/2022] Open
Abstract
APDS2 is caused by mutations in PIK3R1 gene resulting in constitutive PI3Kδ activation. PI3Kδ is predominantly expressed in leukocytes and plays critical roles in regulating immune responses. Here we first derived fibroblast primary cells from a skin biopsy of a patient carrying a heterozygous single T deletion in intron 11 of the PIK3R1 gene. We next present the derivation of an induced pluripotent stem cell (iPS) line using a non-integrative reprogramming technology. Pluripotent-related hallmarks are further shown, including: iPSCs self-renewal and expression of pluripotent and differentiation markers after in vitro differentiation towards embryonic germ layers, assessed by RT-PCR and immunofluorescence.
Collapse
Affiliation(s)
- M Inglés-Ferrándiz
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain; Research Unit, Basque Center for Blood Transfusion and Human Tissues, Osakidetza, Galdakao, Spain
| | - M Martin-Inaraja
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain; Research Unit, Basque Center for Blood Transfusion and Human Tissues, Osakidetza, Galdakao, Spain
| | - L Herrera
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain; Research Unit, Basque Center for Blood Transfusion and Human Tissues, Osakidetza, Galdakao, Spain
| | - M Villaverde
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain; Research Unit, Basque Center for Blood Transfusion and Human Tissues, Osakidetza, Galdakao, Spain
| | - S Santos
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain; Research Unit, Basque Center for Blood Transfusion and Human Tissues, Osakidetza, Galdakao, Spain
| | - M A Vesga
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain; Research Unit, Basque Center for Blood Transfusion and Human Tissues, Osakidetza, Galdakao, Spain
| | - E Garreta
- Pluripotency for Organ Regeneration, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain. University of Barcelona, Barcelona, Spain
| | - I Martín-Ruiz
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio 48160, Spain
| | - A M Aransay
- Genomic Analysis Platform, CIC bioGUNE-BRTA, Derio, 48160, Spain; CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - J Anguita
- Inflammation and Macrophage Plasticity Laboratory, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio 48160, Spain; Ikerbasque, Basque Foundation for Science, Bilbao 48013, Spain
| | - B Barreña
- Genetics Unit, Hospital de Basurto, Bilbao, Spain
| | - L M Allende
- Immunology Department, University Hospital 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), School of Medicine, University Hospital 12 de Octubre, Complutense University of Madrid, Madrid, Spain
| | - L I Gonzalez-Granado
- Primary Immunodeficiencies Unit, Pediatrics, Hospital 12 Octubre (imas12), Complutense University School of Medicine, Madrid, Spain
| | - C Eguizabal
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain; Research Unit, Basque Center for Blood Transfusion and Human Tissues, Osakidetza, Galdakao, Spain.
| |
Collapse
|
26
|
Lario S, Ramírez-Lázaro MJ, González-Lahera A, Lavín JL, Vila-Casadesús M, Quílez ME, Brunet-Vega A, Lozano JJ, Aransay AM, Calvet X. Cross-sectional study of human coding- and non-coding RNAs in progressive stages of Helicobacter pylori infection. Sci Data 2020; 7:296. [PMID: 32901043 PMCID: PMC7479617 DOI: 10.1038/s41597-020-00636-6] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/19/2020] [Indexed: 11/09/2022] Open
Abstract
Helicobacter pylori infects 4.4 billion individuals worldwide and is considered the most important etiologic agent for peptic ulcers and gastric cancer. Individual response to H. pylori infection is complex and depends on complex interactions between host and environmental factors. The pathway towards gastric cancer is a sequence of events known as Correa's model of gastric carcinogenesis, a stepwise inflammatory process from normal mucosa to chronic-active gastritis, atrophy, metaplasia and gastric adenocarcinoma. This study examines gastric clinical specimens representing different steps of the Correa pathway with the aim of identifying the expression profiles of coding- and non-coding RNAs that may have a role in Correa's model of gastric carcinogenesis. We screened for differentially expressed genes in gastric biopsies by employing RNAseq, microarrays and qRT-PCR. Here we provide a detailed description of the experiments, methods and results generated. The datasets may help other scientists and clinicians to find new clues to the pathogenesis of H. pylori and the mechanisms of progression of the infection to more severe gastric diseases. Data is available via ArrayExpress.
Collapse
Affiliation(s)
- Sergio Lario
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain. .,Digestive Diseases Service, Hospital Universitari Parc Taulí, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain.
| | - María J Ramírez-Lázaro
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain.,Digestive Diseases Service, Hospital Universitari Parc Taulí, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Aintzane González-Lahera
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain.,Genome Analysis Platform, CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, Spain
| | - José L Lavín
- Genome Analysis Platform, CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, Spain
| | - Maria Vila-Casadesús
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain.,Bioinformatics Platform, CIBEREHD, Barcelona, Spain
| | - María E Quílez
- Digestive Diseases Service, Hospital Universitari Parc Taulí, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Anna Brunet-Vega
- Oncology Service, Hospital Universitari Parc Taulí, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Juan J Lozano
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain.,Bioinformatics Platform, CIBEREHD, Barcelona, Spain
| | - Ana M Aransay
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain.,Genome Analysis Platform, CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, Spain
| | - Xavier Calvet
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain.,Digestive Diseases Service, Hospital Universitari Parc Taulí, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain.,Departament de Medicina, UAB, Sabadell, Spain
| |
Collapse
|
27
|
Rodriguez RM, Suarez-Alvarez B, Lavín JL, Ascensión AM, Gonzalez M, Lozano JJ, Raneros AB, Bulnes PD, Vidal-Castiñeira JR, Huidobro C, Martin-Martin C, Sanz AB, Ruiz-Ortega M, Puig-Kröger A, Corbí AL, Araúzo-Bravo MJ, Aransay AM, Lopez-Larrea C. Signal Integration and Transcriptional Regulation of the Inflammatory Response Mediated by the GM-/M-CSF Signaling Axis in Human Monocytes. Cell Rep 2019; 29:860-872.e5. [DOI: 10.1016/j.celrep.2019.09.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 06/27/2019] [Accepted: 09/11/2019] [Indexed: 12/15/2022] Open
|
28
|
Clos-Garcia M, Andrés-Marin N, Fernández-Eulate G, Abecia L, Lavín JL, van Liempd S, Cabrera D, Royo F, Valero A, Errazquin N, Vega MCG, Govillard L, Tackett MR, Tejada G, Gónzalez E, Anguita J, Bujanda L, Orcasitas AMC, Aransay AM, Maíz O, López de Munain A, Falcón-Pérez JM. Gut microbiome and serum metabolome analyses identify molecular biomarkers and altered glutamate metabolism in fibromyalgia. EBioMedicine 2019; 46:499-511. [PMID: 31327695 PMCID: PMC6710987 DOI: 10.1016/j.ebiom.2019.07.031] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [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: 03/12/2019] [Revised: 06/24/2019] [Accepted: 07/10/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Fibromyalgia is a complex, relatively unknown disease characterised by chronic, widespread musculoskeletal pain. The gut-brain axis connects the gut microbiome with the brain through the enteric nervous system (ENS); its disruption has been associated with psychiatric and gastrointestinal disorders. To gain an insight into the pathogenesis of fibromyalgia and identify diagnostic biomarkers, we combined different omics techniques to analyse microbiome and serum composition. METHODS We collected faeces and blood samples to study the microbiome, the serum metabolome and circulating cytokines and miRNAs from a cohort of 105 fibromyalgia patients and 54 age- and environment-matched healthy individuals. We sequenced the V3 and V4 regions of the 16S rDNA gene from faeces samples. UPLC-MS metabolomics and custom multiplex cytokine and miRNA analysis (FirePlex™ technology) were used to examine sera samples. Finally, we combined the different data types to search for potential biomarkers. RESULTS We found that the diversity of bacteria is reduced in fibromyalgia patients. The abundance of the Bifidobacterium and Eubacterium genera (bacteria participating in the metabolism of neurotransmitters in the host) in these patients was significantly reduced. The serum metabolome analysis revealed altered levels of glutamate and serine, suggesting changes in neurotransmitter metabolism. The combined serum metabolomics and gut microbiome datasets showed a certain degree of correlation, reflecting the effect of the microbiome on metabolic activity. We also examined the microbiome and serum metabolites, cytokines and miRNAs as potential sources of molecular biomarkers of fibromyalgia. CONCLUSIONS Our results show that the microbiome analysis provides more significant biomarkers than the other techniques employed in the work. Gut microbiome analysis combined with serum metabolomics can shed new light onto the pathogenesis of fibromyalgia. We provide a list of bacteria whose abundance changes in this disease and propose several molecules as potential biomarkers that can be used to evaluate the current diagnostic criteria.
Collapse
Affiliation(s)
- Marc Clos-Garcia
- Exosomes Laboratory, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Derio, Spain; Department of Gastroenterology, Instituto Biodonostia, Universidad del País Vasco (UPV/EHU), CIBERehd (Centro de investigación en red de enfermedades hepáticas y digestiva) San Sebastian, Spain.
| | | | - Gorka Fernández-Eulate
- Department of Neurology, Donostia University Hospital, San Sebastian, Spain; Neuroscience Area, Biodonostia Health Research Institute, San Sebastian, Spain.
| | - Leticia Abecia
- Macrophage and Tick Vaccine Laboratory, CIC bioGUNE, Bizkaia Technology Park, Derio, Spain.
| | - José L Lavín
- Bioinformatics Unit, CIC bioGUNE, Bizkaia Technology Park, Derio, Spain.
| | - Sebastiaan van Liempd
- Metabolomics Platform, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Derio, Spain.
| | - Diana Cabrera
- Metabolomics Platform, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Derio, Spain.
| | - Félix Royo
- Exosomes Laboratory, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Derio, Spain.
| | - Alejandro Valero
- Department of Rheumatology, Donostia University Hospital, San Sebastian, Spain.
| | - Nerea Errazquin
- Department of Rheumatology, Gipuzcoa Policlinic, San Sebastian, Spain.
| | | | | | | | | | - Esperanza Gónzalez
- Exosomes Laboratory, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Derio, Spain.
| | - Juan Anguita
- Macrophage and Tick Vaccine Laboratory, CIC bioGUNE, Bizkaia Technology Park, Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
| | - Luis Bujanda
- Department of Gastroenterology, Instituto Biodonostia, Universidad del País Vasco (UPV/EHU), CIBERehd (Centro de investigación en red de enfermedades hepáticas y digestiva) San Sebastian, Spain.
| | | | - Ana M Aransay
- Genome Analysis Platform, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Derio, Spain.
| | - Olga Maíz
- Department of Rheumatology, Donostia University Hospital, San Sebastian, Spain.
| | - Adolfo López de Munain
- Department of Neurology, Donostia University Hospital, San Sebastian, Spain; Neuroscience Area, Biodonostia Health Research Institute, San Sebastian, Spain; Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Spain; Department of Neurosciences, University of Basque Country UPV/EHU, San Sebastian, Spain.
| | - Juan Manuel Falcón-Pérez
- Exosomes Laboratory, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Derio, Spain; Metabolomics Platform, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
| |
Collapse
|
29
|
Lorén V, Garcia-Jaraquemada A, Naves JE, Carmona X, Mañosa M, Aransay AM, Lavin JL, Sánchez I, Cabré E, Manyé J, Domènech E. ANP32E, a Protein Involved in Steroid-Refractoriness in Ulcerative Colitis, Identified by a Systems Biology Approach. J Crohns Colitis 2019; 13:351-361. [PMID: 30329026 DOI: 10.1093/ecco-jcc/jjy171] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Steroid-refractoriness is a common and unpredictable phenomenon in ulcerative colitis [UC], but there are no conclusive studies on the molecular functions involved. We aimed to assess the mechanism of action related to steroid failure by integrating transcriptomic data from UC patients, and updated molecular data on UC and glucocorticoids. METHODS MicroRNA [miRNA] and mRNA expression were evaluated by sequencing and microarrays, respectively, from rectal biopsies of patients with moderately-to-severe active UC, obtained before and on the third day of steroid treatment. The differential results were integrated into the mathematical models generated by a systems biology approach. RESULTS This computational approach identified 18 proteins that stand out either by being associated with the mechanism of action or by providing a means to classify the patients according to steroid response. Their biological functions have been linked to inflammation, glucocorticoid-induced transcription and angiogenesis. All the selected proteins except ANP32E [a chaperone which has been linked to the exchange of H2A.z histone and promotes glucocorticoid receptor-induced transcription] had previously been related to UC and/or glucocorticoid-induced biological actions. Western blot and immunofluorescence assays confirmed the implication of this chaperone in steroid failure in patients with active UC. CONCLUSIONS A systems biology approach allowed us to identify a comprehensive mechanism of action of steroid-refractoriness, highlighting the key role of steroid-induced transcription and the potential implication of ANP32E in this phenomenon.
Collapse
Affiliation(s)
- V Lorén
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain
| | - A Garcia-Jaraquemada
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain
| | - J E Naves
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain
| | - X Carmona
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain
| | - M Mañosa
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain.,Gastroenterology Department, Germans Trias i Pujol University Hospital, Badalona, Catalonia, Spain
| | - A M Aransay
- Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain.,Genome Analysis Platform, CIC bioGUNE, Derio, Bizkaia, Spain
| | - J L Lavin
- Genome Analysis Platform, CIC bioGUNE, Derio, Bizkaia, Spain
| | - I Sánchez
- Functional Biology and Experimental Therapeutics Laboratory, Functional and Translational Neurogenetics Unit, Department of Neurosciences, Germans Trias i Pujol Research Institute, Badalona, Catalonia, Spain
| | - E Cabré
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain.,Gastroenterology Department, Germans Trias i Pujol University Hospital, Badalona, Catalonia, Spain
| | - J Manyé
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain
| | - E Domènech
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain.,Gastroenterology Department, Germans Trias i Pujol University Hospital, Badalona, Catalonia, Spain
| |
Collapse
|
30
|
Sánchez-Morán M, Hernández JA, Duñabeitia JA, Estévez A, Bárcena L, González-Lahera A, Bajo MT, Fuentes LJ, Aransay AM, Carreiras M. Correction: Genetic association study of dyslexia and ADHD candidate genes in a Spanish cohort: Implications of comorbid samples. PLoS One 2018; 13:e0209718. [PMID: 30566519 PMCID: PMC6300281 DOI: 10.1371/journal.pone.0209718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
31
|
Sánchez-Morán M, Hernández JA, Duñabeitia JA, Estévez A, Bárcena L, González-Lahera A, Bajo MT, Fuentes LJ, Aransay AM, Carreiras M. Genetic association study of dyslexia and ADHD candidate genes in a Spanish cohort: Implications of comorbid samples. PLoS One 2018; 13:e0206431. [PMID: 30379906 PMCID: PMC6209299 DOI: 10.1371/journal.pone.0206431] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 10/02/2017] [Accepted: 10/13/2018] [Indexed: 01/21/2023] Open
Abstract
Dyslexia and attention deficit hyperactivity disorder (ADHD) are two complex neuro-behaviorally disorders that co-occur more often than expected, so that reading disability has been linked to inattention symptoms. We examined 4 SNPs located on genes previously associated to dyslexia (KIAA0319, DCDC2, DYX1C1 and FOXP2) and 3 SNPs within genes related to ADHD (COMT, MAOA and DBH) in a cohort of Spanish children (N = 2078) that met the criteria of having one, both or none of these disorders (dyslexia and ADHD). We used a case-control approach comparing different groups of samples based on each individual diagnosis. In addition, we also performed a quantitative trait analysis with psychometric measures on the general population (N = 3357). The results indicated that the significance values for some markers change depending on the phenotypic groups compared and/or when considering pair-wise marker interactions. Furthermore, our quantitative trait study showed significant genetic associations with specific cognitive processes. These outcomes advocate the importance of establishing rigorous and homogeneous criteria for the diagnosis of cognitive disorders, as well as the relevance of considering cognitive endophenotypes.
Collapse
Affiliation(s)
- Mirian Sánchez-Morán
- BCBL-Basque Center on Cognition Brain and Language, Donostia-San Sebastian, Gipuzkoa, Spain
- CIC bioGUNE, Derio, Bizkaia, Spain
| | | | - Jon Andoni Duñabeitia
- BCBL-Basque Center on Cognition Brain and Language, Donostia-San Sebastian, Gipuzkoa, Spain
| | | | | | | | - María Teresa Bajo
- Research Center for Brain, Mind & Behavior, Universidad de Granada, Granada, Spain
| | | | - Ana M. Aransay
- CIC bioGUNE, Derio, Bizkaia, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Manuel Carreiras
- BCBL-Basque Center on Cognition Brain and Language, Donostia-San Sebastian, Gipuzkoa, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Universidad del Pais Vasco UPV/EHU, Leioa, Bizkaia, Spain
| |
Collapse
|
32
|
Fernández-Ramos D, Fernández-Tussy P, Lopitz-Otsoa F, Gutiérrez-de-Juan V, Navasa N, Barbier-Torres L, Zubiete-Franco I, Simón J, Fernández AF, Arbelaiz A, Aransay AM, Lavín JL, Beraza N, Perugorria MJ, Banales JM, Villa E, Fraga MF, Anguita J, Avila MA, Berasain C, Iruzibieta P, Crespo J, Lu SC, Varela-Rey M, Mato JM, Delgado TC, Martínez-Chantar ML. MiR-873-5p acts as an epigenetic regulator in early stages of liver fibrosis and cirrhosis. Cell Death Dis 2018; 9:958. [PMID: 30237481 PMCID: PMC6148053 DOI: 10.1038/s41419-018-1014-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [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: 06/01/2018] [Revised: 08/29/2018] [Accepted: 08/31/2018] [Indexed: 02/07/2023]
Abstract
Glycine N-methyltransferase (GNMT) is the most abundant methyltransferase in the liver and a master regulator of the transmethylation flux. GNMT downregulation leads to loss of liver function progressing to fibrosis, cirrhosis, and hepatocellular carcinoma. Moreover, GNMT deficiency aggravates cholestasis-induced fibrogenesis. To date, little is known about the mechanisms underlying downregulation of GNMT levels in hepatic fibrosis and cirrhosis. On this basis, microRNAs are epigenetic regulatory elements that play important roles in liver pathology. In this work, we aim to study the regulation of GNMT by microRNAs during liver fibrosis and cirrhosis. Luciferase assay on the 3ʹUTR-Gnmt was used to confirm in silico analysis showing that GNMT is potentially targeted by the microRNA miR-873-5p. Correlation between GNMT and miR-873-5p in human cholestasis and cirrhosis together with miR-873-5p inhibition in vivo in different mouse models of liver cholestasis and fibrosis [bile duct ligation and Mdr2 (Abcb4)-/- mouse] were then assessed. The analysis of liver tissue from cirrhotic and cholestatic patients, as well as from the animal models, showed that miR-873-5p inversely correlated with the expression of GNMT. Importantly, high circulating miR-873-5p was also detected in cholestastic and cirrhotic patients. Preclinical studies with anti-miR-873-5p treatment in bile duct ligation and Mdr2-/- mice recovered GNMT levels in association with ameliorated inflammation and fibrosis mainly by counteracting hepatocyte apoptosis and cholangiocyte proliferation. In conclusion, miR-873-5p emerges as a novel marker for liver fibrosis, cholestasis, and cirrhosis and therapeutic approaches based on anti-miR-873-5p may be effective treatments for liver fibrosis and cholestatic liver disease.
Collapse
Affiliation(s)
- David Fernández-Ramos
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias, Derio, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Pablo Fernández-Tussy
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias, Derio, Bizkaia, Spain
| | - Fernando Lopitz-Otsoa
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias, Derio, Bizkaia, Spain
| | | | - Nicolás Navasa
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias, Derio, Bizkaia, Spain
| | - Lucía Barbier-Torres
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias, Derio, Bizkaia, Spain
| | - Imanol Zubiete-Franco
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias, Derio, Bizkaia, Spain
| | - Jorge Simón
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias, Derio, Bizkaia, Spain
| | - Agustín F Fernández
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, University of Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (IISPA), Oviedo, Spain
| | - Ander Arbelaiz
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute-Donostia University Hospital-University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Ana M Aransay
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias, Derio, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - José Luis Lavín
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias, Derio, Bizkaia, Spain
| | - Naiara Beraza
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias, Derio, Bizkaia, Spain
| | - María J Perugorria
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.,Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute-Donostia University Hospital-University of the Basque Country (UPV/EHU), San Sebastian, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Jesus M Banales
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.,Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute-Donostia University Hospital-University of the Basque Country (UPV/EHU), San Sebastian, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Erica Villa
- Department of Gastroenterology, Azienda Ospedaliero-Universitaria & University of Modena and Reggio Emilia, Modena, Italy
| | - Mario F Fraga
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC)-Universidad de Oviedo-Principado de Asturias, Oviedo, Spain
| | - Juan Anguita
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Matias A Avila
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.,Hepatology Programme, CIMA-University of Navarra, IdiSNA, Pamplona, Spain
| | - Carmen Berasain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.,Hepatology Programme, CIMA-University of Navarra, IdiSNA, Pamplona, Spain
| | - Paula Iruzibieta
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.,Department of Gastroenterology and Hepatology, Marqués de Valdecilla University Hospital. Infection, Immunity and Digestive Pathology Group, Research Institute Marqués de Valdecilla (IDIVAL), Santander, Spain
| | - Javier Crespo
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.,Department of Gastroenterology and Hepatology, Marqués de Valdecilla University Hospital. Infection, Immunity and Digestive Pathology Group, Research Institute Marqués de Valdecilla (IDIVAL), Santander, Spain
| | - Shelly C Lu
- Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Marta Varela-Rey
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias, Derio, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - José M Mato
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias, Derio, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Teresa C Delgado
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias, Derio, Bizkaia, Spain.
| | - María L Martínez-Chantar
- CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias, Derio, Bizkaia, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.
| |
Collapse
|
33
|
Cortazar AR, Torrano V, Martín-Martín N, Caro-Maldonado A, Camacho L, Hermanova I, Guruceaga E, Lorenzo-Martín LF, Caloto R, Gomis RR, Apaolaza I, Quesada V, Trka J, Gomez-Muñoz A, Vincent S, Bustelo XR, Planes FJ, Aransay AM, Carracedo A. CANCERTOOL: A Visualization and Representation Interface to Exploit Cancer Datasets. Cancer Res 2018; 78:6320-6328. [PMID: 30232219 DOI: 10.1158/0008-5472.can-18-1669] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/02/2018] [Accepted: 09/06/2018] [Indexed: 11/16/2022]
Abstract
With the advent of OMICs technologies, both individual research groups and consortia have spear-headed the characterization of human samples of multiple pathophysiologic origins, resulting in thousands of archived genomes and transcriptomes. Although a variety of web tools are now available to extract information from OMICs data, their utility has been limited by the capacity of nonbioinformatician researchers to exploit the information. To address this problem, we have developed CANCERTOOL, a web-based interface that aims to overcome the major limitations of public transcriptomics dataset analysis for highly prevalent types of cancer (breast, prostate, lung, and colorectal). CANCERTOOL provides rapid and comprehensive visualization of gene expression data for the gene(s) of interest in well-annotated cancer datasets. This visualization is accompanied by generation of reports customized to the interest of the researcher (e.g., editable figures, detailed statistical analyses, and access to raw data for reanalysis). It also carries out gene-to-gene correlations in multiple datasets at the same time or using preset patient groups. Finally, this new tool solves the time-consuming task of performing functional enrichment analysis with gene sets of interest using up to 11 different databases at the same time. Collectively, CANCERTOOL represents a simple and freely accessible interface to interrogate well-annotated datasets and obtain publishable representations that can contribute to refinement and guidance of cancer-related investigations at all levels of hypotheses and design.Significance: In order to facilitate access of research groups without bioinformatics support to public transcriptomics data, we have developed a free online tool with an easy-to-use interface that allows researchers to obtain quality information in a readily publishable format. Cancer Res; 78(21); 6320-8. ©2018 AACR.
Collapse
Affiliation(s)
- Ana R Cortazar
- CIC bioGUNE, Bizkaia Technology Park, Bizkaia, Spain.,CIBERONC, Madrid, Spain
| | - Veronica Torrano
- CIC bioGUNE, Bizkaia Technology Park, Bizkaia, Spain.,CIBERONC, Madrid, Spain
| | | | | | - Laura Camacho
- CIC bioGUNE, Bizkaia Technology Park, Bizkaia, Spain.,Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | | | - Elizabeth Guruceaga
- CIBERONC, Madrid, Spain.,Bioinformatics Unit, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Luis F Lorenzo-Martín
- CIBERONC, Madrid, Spain.,Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca, Salamanca, Spain
| | - Ruben Caloto
- CIBERONC, Madrid, Spain.,Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca, Salamanca, Spain
| | - Roger R Gomis
- CIBERONC, Madrid, Spain.,Oncology Programme, Institute for Research in Biomedicine (IRB-Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Iñigo Apaolaza
- University of Navarra, Tecnun School of Engineering, San Sebastián, Spain
| | - Victor Quesada
- CIBERONC, Madrid, Spain.,Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Oviedo, Spain
| | - Jan Trka
- CLIP-Childhood Leukaemia Investigation Prague and Second Faculty of Medicine, Charles University, Prague, Czech Republic.,University Hospital Motol, Prague, Czech Republic
| | - Antonio Gomez-Muñoz
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Silvestre Vincent
- CIBERONC, Madrid, Spain.,University of Navarra, Department of Histology and Pathology, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.,Center for Applied Medical Research, Program of Solid Tumors, University of Navarra, Pamplona, Spain
| | - Xose R Bustelo
- CIBERONC, Madrid, Spain.,Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca, Salamanca, Spain
| | - Francisco J Planes
- University of Navarra, Tecnun School of Engineering, San Sebastián, Spain
| | - Ana M Aransay
- CIC bioGUNE, Bizkaia Technology Park, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Arkaitz Carracedo
- CIC bioGUNE, Bizkaia Technology Park, Bizkaia, Spain. .,CIBERONC, Madrid, Spain.,Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), Bilbao, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| |
Collapse
|
34
|
Tomás-Cortázar J, Plaza-Vinuesa L, de Las Rivas B, Lavín JL, Barriales D, Abecia L, Mancheño JM, Aransay AM, Muñoz R, Anguita J, Rodríguez H. Identification of a highly active tannase enzyme from the oral pathogen Fusobacterium nucleatum subsp. polymorphum. Microb Cell Fact 2018; 17:33. [PMID: 29482557 PMCID: PMC5828091 DOI: 10.1186/s12934-018-0880-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 02/22/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Tannases are tannin-degrading enzymes that have been described in fungi and bacteria as an adaptative mechanism to overcome the stress conditions associated with the presence of these phenolic compounds. RESULTS We have identified and expressed in E. coli a tannase from the oral microbiota member Fusobacterium nucleatum subs. polymorphum (TanBFnp). TanBFnp is the first tannase identified in an oral pathogen. Sequence analyses revealed that it is closely related to other bacterial tannases. The enzyme exhibits biochemical properties that make it an interesting target for industrial use. TanBFnp has one of the highest specific activities of all bacterial tannases described to date and shows optimal biochemical properties such as a high thermal stability: the enzyme keeps 100% of its activity after prolonged incubations at different temperatures up to 45 °C. TanBFnp also shows a wide temperature range of activity, maintaining above 80% of its maximum activity between 22 and 55 °C. The use of a panel of 27 esters of phenolic acids demonstrated activity of TanBFnp only against esters of gallic and protocatechuic acid, including tannic acid, gallocatechin gallate and epigallocatechin gallate. Overall, TanBFnp possesses biochemical properties that make the enzyme potentially useful in biotechnological applications. CONCLUSIONS We have identified and characterized a metabolic enzyme from the oral pathogen Fusobacterium nucleatum subsp. polymorphum. The biochemical properties of TanBFnp suggest that it has a major role in the breakdown of complex food tannins during oral processing. Our results also provide some clues regarding its possible participation on bacterial survival in the oral cavity. Furthermore, the characteristics of this enzyme make it of potential interest for industrial use.
Collapse
Affiliation(s)
| | - Laura Plaza-Vinuesa
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN)-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Blanca de Las Rivas
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN)-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - José Luis Lavín
- Genome Analysis Platform, CIC bioGUNE, Derio, Bizkaia, Spain
| | - Diego Barriales
- Macrophage and Tick Vaccine Laboratory, CIC bioGUNE, Derio, Bizkaia, Spain
| | - Leticia Abecia
- Macrophage and Tick Vaccine Laboratory, CIC bioGUNE, Derio, Bizkaia, Spain
| | - José Miguel Mancheño
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física "Rocasolano" (IQFR-CSIC), Madrid, Spain
| | - Ana M Aransay
- Genome Analysis Platform, CIC bioGUNE, Derio, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Rosario Muñoz
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN)-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Juan Anguita
- Macrophage and Tick Vaccine Laboratory, CIC bioGUNE, Derio, Bizkaia, Spain. .,Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia, Spain.
| | - Héctor Rodríguez
- Macrophage and Tick Vaccine Laboratory, CIC bioGUNE, Derio, Bizkaia, Spain.
| |
Collapse
|
35
|
Zabala-Letona A, Arruabarrena-Aristorena A, Martín-Martín N, Fernandez-Ruiz S, Sutherland JD, Clasquin M, Tomas-Cortazar J, Jimenez J, Torres I, Quang P, Ximenez-Embun P, Bago R, Ugalde-Olano A, Loizaga-Iriarte A, Lacasa-Viscasillas I, Unda M, Torrano V, Cabrera D, van Liempd SM, Cendon Y, Castro E, Murray S, Revandkar A, Alimonti A, Zhang Y, Barnett A, Lein G, Pirman D, Cortazar AR, Arreal L, Prudkin L, Astobiza I, Valcarcel-Jimenez L, Zuñiga-García P, Fernandez-Dominguez I, Piva M, Caro-Maldonado A, Sánchez-Mosquera P, Castillo-Martín M, Serra V, Beraza N, Gentilella A, Thomas G, Azkargorta M, Elortza F, Farràs R, Olmos D, Efeyan A, Anguita J, Muñoz J, Falcón-Pérez JM, Barrio R, Macarulla T, Mato JM, Martinez-Chantar ML, Cordon-Cardo C, Aransay AM, Marks K, Baselga J, Tabernero J, Nuciforo P, Manning BD, Marjon K, Carracedo A. Erratum: Corrigendum: mTORC1-dependent AMD1 regulation sustains polyamine metabolism in prostate cancer. Nature 2018; 554:554. [DOI: 10.1038/nature25470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
36
|
Martín-Martín N, Zabala-Letona A, Fernández-Ruiz S, Arreal L, Camacho L, Castillo-Martin M, Cortazar AR, Torrano V, Astobiza I, Zúñiga-García P, Ugalde-Olano A, Loizaga-Iriarte A, Unda M, Valcárcel-Jiménez L, Arruabarrena-Aristorena A, Piva M, Sánchez-Mosquera P, Aransay AM, Gomez-Muñoz A, Barrio R, Sutherland JD, Carracedo A. PPARδ Elicits Ligand-Independent Repression of Trefoil Factor Family to Limit Prostate Cancer Growth. Cancer Res 2017; 78:399-409. [DOI: 10.1158/0008-5472.can-17-0908] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 09/18/2017] [Accepted: 11/14/2017] [Indexed: 11/16/2022]
|
37
|
Cortazar AR, Oguiza JA, Aransay AM, Lavín JL. VerSeDa: vertebrate secretome database. Database (Oxford) 2017; 2017:3052689. [PMID: 28365718 PMCID: PMC5467544 DOI: 10.1093/database/baw171] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/28/2016] [Indexed: 12/11/2022]
Abstract
Based on the current tools, de novo secretome (full set of proteins secreted by an organism) prediction is a time consuming bioinformatic task that requires a multifactorial analysis in order to obtain reliable in silico predictions. Hence, to accelerate this process and offer researchers a reliable repository where secretome information can be obtained for vertebrates and model organisms, we have developed VerSeDa (Vertebrate Secretome Database). This freely available database stores information about proteins that are predicted to be secreted through the classical and non-classical mechanisms, for the wide range of vertebrate species deposited at the NCBI, UCSC and ENSEMBL sites. To our knowledge, VerSeDa is the only state-of-the-art database designed to store secretome data from multiple vertebrate genomes, thus, saving an important amount of time spent in the prediction of protein features that can be retrieved from this repository directly. Database URL: VerSeDa is freely available at http://genomics.cicbiogune.es/VerSeDa/index.php
Collapse
Affiliation(s)
- Ana R Cortazar
- Genome Analysis Platform, CIC bioGUNE & CIBERehd, Bizkaia Technology Park, 48160 Derio, Spain
| | - José A Oguiza
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006 Pamplona, Spain
| | - Ana M Aransay
- Genome Analysis Platform, CIC bioGUNE & CIBERehd, Bizkaia Technology Park, 48160 Derio, Spain
| | - José L Lavín
- Genome Analysis Platform, CIC bioGUNE & CIBERehd, Bizkaia Technology Park, 48160 Derio, Spain
| |
Collapse
|
38
|
Caro-Maldonado A, Camacho L, Zabala-Letona A, Torrano V, Fernández-Ruiz S, Zamacola-Bascaran K, Arreal L, Valcárcel-Jiménez L, Martín-Martín N, Flores JM, Cortazar AR, Zúñiga-García P, Arruabarrena-Aristorena A, Guillaumond F, Cabrera D, Falcón-Perez JM, Aransay AM, Gomez-Muñoz A, Olivan M, Morote J, Carracedo A. Low-dose statin treatment increases prostate cancer aggressiveness. Oncotarget 2017; 9:1494-1504. [PMID: 29416709 PMCID: PMC5788577 DOI: 10.18632/oncotarget.22217] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 07/13/2017] [Accepted: 10/13/2017] [Indexed: 11/25/2022] Open
Abstract
Prostate cancer is diagnosed late in life, when co-morbidities are frequent. Among them, hypertension, hypercholesterolemia, diabetes or metabolic syndrome exhibit an elevated incidence. In turn, prostate cancer patients frequently undergo chronic pharmacological treatments that could alter disease initiation, progression and therapy response. Here we show that treatment with anti-cholesterolemic drugs, statins, at doses achieved in patients, enhance the pro-tumorigenic activity of obesogenic diets. In addition, the use of a mouse model of prostate cancer and human prostate cancer xenografts revealed that in vivo simvastatin administration alone increases prostate cancer aggressiveness. In vitro cell line systems supported the notion that this phenomenon occurs, at least in part, through the direct action on cancer cells of low doses of statins, in range of what is observed in human plasma. In sum, our results reveal a prostate cancer experimental system where statins exhibit an undesirable effect, and warrant further research to address the relevance and implications of this observation in human prostate cancer.
Collapse
Affiliation(s)
| | - Laura Camacho
- CIC bioGUNE, Bizkaia Technology Park, Derio, Spain.,Biochemistry and Molecular Biology Department, University of the Basque Country, Bilbao, Spain
| | | | - Verónica Torrano
- CIC bioGUNE, Bizkaia Technology Park, Derio, Spain.,CIBERONC, Madrid, Spain
| | | | | | - Leire Arreal
- CIC bioGUNE, Bizkaia Technology Park, Derio, Spain
| | | | | | - Juana M Flores
- Department of Animal Medicine and Surgery, School of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
| | | | | | | | - Fabienne Guillaumond
- Centre de Recherche en Cancérologie de Marseille, U1068, Institut National de la Santé et de la Recherche Médicale, Paris, France.,Institut Paoli-Calmettes, Marseille, France.,UMR 7258, Centre National de la Recherche Scientifique, Paris, France.,Université Aix-Marseille, Marseille, France
| | | | - Juan M Falcón-Perez
- CIC bioGUNE, Bizkaia Technology Park, Derio, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain.,IKERBASQUE, Basque foundation for science, Bilbao, Spain
| | - Ana M Aransay
- CIC bioGUNE, Bizkaia Technology Park, Derio, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
| | - Antonio Gomez-Muñoz
- Biochemistry and Molecular Biology Department, University of the Basque Country, Bilbao, Spain
| | - Mireia Olivan
- Department of Urology and Research Group in Urology, Vall d´Hebron Hospital, Vall d´Hebron Research Institute, and Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juan Morote
- Department of Urology and Research Group in Urology, Vall d´Hebron Hospital, Vall d´Hebron Research Institute, and Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Arkaitz Carracedo
- CIC bioGUNE, Bizkaia Technology Park, Derio, Spain.,Biochemistry and Molecular Biology Department, University of the Basque Country, Bilbao, Spain.,CIBERONC, Madrid, Spain.,IKERBASQUE, Basque foundation for science, Bilbao, Spain
| |
Collapse
|
39
|
Iruarrizaga-Lejarreta M, Varela-Rey M, Fernández-Ramos D, Martínez-Arranz I, Delgado TC, Simon J, Juan VGD, delaCruz-Villar L, Azkargorta M, Lavin JL, Mayo R, Van Liempd SM, Aurrekoetxea I, Buqué X, Cave DD, Peña A, Rodríguez-Cuesta J, Aransay AM, Elortza F, Falcón-Pérez JM, Aspichueta P, Hayardeny L, Noureddin M, Sanyal AJ, Alonso C, Anguita J, Martínez-Chantar ML, Lu SC, Mato JM. Role of Aramchol in steatohepatitis and fibrosis in mice. Hepatol Commun 2017; 1:911-927. [PMID: 29159325 PMCID: PMC5691602 DOI: 10.1002/hep4.1107] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [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] [Indexed: 12/15/2022] Open
Abstract
Nonalcoholic steatohepatitis (NASH) is the advanced form of nonalcoholic fatty liver disease (NAFLD) that sets the stage for further liver damage. The mechanism for the progression of NASH involves multiple parallel hits, including oxidative stress, mitochondrial dysfunction, inflammation, and others. Manipulation of any of these pathways may be an approach to prevent NASH development and progression. Arachidyl‐amido cholanoic acid (Aramchol) is presently in a phase IIb NASH study. The aim of the present study was to investigate Aramchol's mechanism of action and its effect on fibrosis using the methionine‐ and choline‐deficient (MCD) diet model of NASH. We collected liver and serum from mice fed an MCD diet containing 0.1% methionine (0.1MCD) for 4 weeks; these mice developed steatohepatitis and fibrosis. We also collected liver and serum from mice receiving a control diet, and metabolomes and proteomes were determined for both groups. The 0.1MCD‐fed mice were given Aramchol (5 mg/kg/day for the last 2 weeks), and liver samples were analyzed histologically. Aramchol administration reduced features of steatohepatitis and fibrosis in 0.1MCD‐fed mice. Aramchol down‐regulated stearoyl‐coenyzme A desaturase 1, a key enzyme involved in triglyceride biosynthesis and the loss of which enhances fatty acid β‐oxidation. Aramchol increased the flux through the transsulfuration pathway, leading to a rise in glutathione (GSH) and the GSH/oxidized GSH ratio, the main cellular antioxidant that maintains intracellular redox status. Comparison of the serum metabolomic pattern between 0.1MCD‐fed mice and patients with NAFLD showed a substantial overlap. Conclusion: Aramchol treatment improved steatohepatitis and fibrosis by 1) decreasing stearoyl‐coenyzme A desaturase 1 and 2) increasing the flux through the transsulfuration pathway maintaining cellular redox homeostasis. We also demonstrated that the 0.1MCD model resembles the metabolic phenotype observed in about 50% of patients with NAFLD, which supports the potential use of Aramchol in NASH treatment. (Hepatology Communications 2017;1:911–927)
Collapse
Affiliation(s)
| | - Marta Varela-Rey
- CIC bioGUNE, CIBERehd, Parque Tecnológico de Bizkaia, Derio, Spain
| | | | | | - Teresa C Delgado
- CIC bioGUNE, CIBERehd, Parque Tecnológico de Bizkaia, Derio, Spain
| | - Jorge Simon
- CIC bioGUNE, CIBERehd, Parque Tecnológico de Bizkaia, Derio, Spain
| | | | | | - Mikel Azkargorta
- CIC bioGUNE, CIBERehd, Parque Tecnológico de Bizkaia, Derio, Spain
| | - José L Lavin
- CIC bioGUNE, CIBERehd, Parque Tecnológico de Bizkaia, Derio, Spain
| | - Rebeca Mayo
- OWL Metabolomics, Parque Tecnológico de Bizkaia, Derio, Spain
| | | | - Igor Aurrekoetxea
- Department of Physiology, University of the Basque Country, Biocruces Research Institute, Leioa, Spain
| | - Xabier Buqué
- Department of Physiology, University of the Basque Country, Biocruces Research Institute, Leioa, Spain
| | | | - Arantza Peña
- CIC bioGUNE, CIBERehd, Parque Tecnológico de Bizkaia, Derio, Spain
| | | | - Ana M Aransay
- CIC bioGUNE, CIBERehd, Parque Tecnológico de Bizkaia, Derio, Spain
| | - Felix Elortza
- CIC bioGUNE, CIBERehd, Parque Tecnológico de Bizkaia, Derio, Spain
| | - Juan M Falcón-Pérez
- CIC bioGUNE, CIBERehd, Parque Tecnológico de Bizkaia, Derio, Spain.,IKERBASQUE Basque Foundation for Science, Bilbao, Spain
| | - Patricia Aspichueta
- Department of Physiology, University of the Basque Country, Biocruces Research Institute, Leioa, Spain
| | | | - Mazen Noureddin
- Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Arun J Sanyal
- Division of Gastroenterology and Hepatology, Virginia Commonwealth University Medical Center, Richmond, USA
| | - Cristina Alonso
- OWL Metabolomics, Parque Tecnológico de Bizkaia, Derio, Spain
| | - Juan Anguita
- CIC bioGUNE, CIBERehd, Parque Tecnológico de Bizkaia, Derio, Spain.,IKERBASQUE Basque Foundation for Science, Bilbao, Spain
| | | | - Shelly C Lu
- Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - José M Mato
- CIC bioGUNE, CIBERehd, Parque Tecnológico de Bizkaia, Derio, Spain
| |
Collapse
|
40
|
Merino-Azpitarte M, Lozano E, Perugorria MJ, Esparza-Baquer A, Erice O, Santos-Laso A, O'Rourke CJ, Andersen JB, Jiménez-Agüero R, Lacasta A, D'Amato M, Briz O, Jalan-Sakrikar N, Huebert RC, Thelen KM, Gradilone SA, Aransay AM, Lavín JL, Fernández-Barrena MG, Matheu A, Marzioni M, Gores GJ, Bujanda L, Marin JJG, Banales JM. SOX17 regulates cholangiocyte differentiation and acts as a tumor suppressor in cholangiocarcinoma. J Hepatol 2017; 67:72-83. [PMID: 28237397 PMCID: PMC5502751 DOI: 10.1016/j.jhep.2017.02.017] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [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: 08/28/2016] [Revised: 01/25/2017] [Accepted: 02/14/2017] [Indexed: 12/28/2022]
Abstract
BACKGROUND & AIMS Cholangiocarcinoma (CCA) is a biliary malignancy linked to genetic and epigenetic abnormalities, such as hypermethylation of SOX17 promoter. Here, the role of SOX17 in cholangiocyte differentiation and cholangiocarcinogenesis was studied. METHODS SOX17 expression/function was evaluated along the differentiation of human induced pluripotent stem cells (iPSC) into cholangiocytes, in the dedifferentiation process of normal human cholangiocytes (NHC) in culture and in cholangiocarcinogenesis. Lentiviruses for SOX17 overexpression or knockdown were used. Gene expression and DNA methylation profiling were performed. RESULTS SOX17 expression is induced in the last stage of cholangiocyte differentiation from iPSC and regulates the acquisition of biliary markers. SOX17 becomes downregulated in NHC undergoing dedifferentiation; experimental SOX17 knockdown in differentiated NHC downregulated biliary markers and promoted baseline and Wnt-dependent proliferation. SOX17 expression is lower in human CCA than in healthy tissue, which correlates with worse survival after tumor resection. In CCA cells, SOX17 overexpression decreased their tumorigenic capacity in murine xenograft models, which was related to increased oxidative stress and apoptosis. In contrast, SOX17 overexpression in NHC did not affect their survival but inhibited their baseline proliferation. In CCA cells, SOX17 inhibited migration, anchorage-independent growth and Wnt/β-catenin-dependent proliferation, and restored the expression of biliary markers and primary cilium length. In human CCA, SOX17 promoter was found hypermethylated and its expression inversely correlates with the methylation grade. In NHC, Wnt3a decreased SOX17 expression in a DNMT-dependent manner, whereas in CCA, DNMT1 inhibition or silencing upregulated SOX17. CONCLUSIONS SOX17 regulates the differentiation and maintenance of the biliary phenotype and functions as a tumor suppressor for CCA, being a potential prognostic marker and a promising therapeutic target. LAY SUMMARY Understanding the molecular mechanisms involved in the pathogenesis of CCA is key in finding new valuable diagnostic and prognostic biomarkers, as well as therapeutic targets. This study provides evidence that SOX17 regulates the differentiation and maintenance of the biliary phenotype, and its downregulation promotes their tumorigenic transformation. SOX17 acts as a tumor suppressor in CCA and its genetic, molecular and/or pharmacological restoration may represent a new promising therapeutic strategy. Moreover, SOX17 expression correlates with the outcome of patients after tumor resection, being a potential prognostic biomarker.
Collapse
Affiliation(s)
- M Merino-Azpitarte
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute – Donostia University Hospital –, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - E Lozano
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute – Donostia University Hospital –, University of the Basque Country (UPV/EHU), San Sebastian, Spain,Experimental Hepatology and Drug Targeting (HEVEFARM), Biomedical Research Institute of Salamanca (IBSAL), University of Salamanca, Salamanca, Spain,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), Spain
| | - MJ Perugorria
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute – Donostia University Hospital –, University of the Basque Country (UPV/EHU), San Sebastian, Spain,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), Spain,IKERBASQUE, Basque Foundation for Science, University of Copenhagen, Copenhagen, Denmark
| | - A Esparza-Baquer
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute – Donostia University Hospital –, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - O Erice
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute – Donostia University Hospital –, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - A Santos-Laso
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute – Donostia University Hospital –, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - CJ O'Rourke
- Biotech Research and Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - JB Andersen
- Biotech Research and Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - R Jiménez-Agüero
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute – Donostia University Hospital –, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - A Lacasta
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute – Donostia University Hospital –, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - M D'Amato
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute – Donostia University Hospital –, University of the Basque Country (UPV/EHU), San Sebastian, Spain,IKERBASQUE, Basque Foundation for Science, University of Copenhagen, Copenhagen, Denmark
| | - O Briz
- Experimental Hepatology and Drug Targeting (HEVEFARM), Biomedical Research Institute of Salamanca (IBSAL), University of Salamanca, Salamanca, Spain,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), Spain
| | - N Jalan-Sakrikar
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - RC Huebert
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - KM Thelen
- The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - SA Gradilone
- The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - AM Aransay
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), Spain,Genome Analysis Platform, CIC bioGUNE, Bizkaia Technology Park, Derio, Spain
| | - JL Lavín
- Genome Analysis Platform, CIC bioGUNE, Bizkaia Technology Park, Derio, Spain
| | | | - A Matheu
- IKERBASQUE, Basque Foundation for Science, University of Copenhagen, Copenhagen, Denmark,Neuro-Oncology Group, Biodonostia Research Institute – Donostia University Hospital –, San Sebastian, Spain
| | - M Marzioni
- Department of Gastroenterology, “Università Politecnica delle Marche”, Ancona, Italy
| | - GJ Gores
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - L Bujanda
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute – Donostia University Hospital –, University of the Basque Country (UPV/EHU), San Sebastian, Spain,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), Spain
| | - JJG Marin
- Experimental Hepatology and Drug Targeting (HEVEFARM), Biomedical Research Institute of Salamanca (IBSAL), University of Salamanca, Salamanca, Spain,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), Spain
| | - JM Banales
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute – Donostia University Hospital –, University of the Basque Country (UPV/EHU), San Sebastian, Spain,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), Spain,IKERBASQUE, Basque Foundation for Science, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
41
|
Alonso C, Fernández-Ramos D, Varela-Rey M, Martínez-Arranz I, Navasa N, Van Liempd SM, Lavin JL, Mayo R, Ilisso CP, de Juan VG, Iruarrizaga-Lejarreta M, delaCruz-Villar L, Mincholé I, Robinson A, Crespo J, Martín-Duce A, Romero-Gomez M, Sann H, Platon J, Van Eyk J, Aspichueta P, Noureddin M, Falcón-Pérez JM, Anguita J, Aransay AM, Martínez-Chantar ML, Lu SC, Mato JM. Metabolomic Identification of Subtypes of Nonalcoholic Steatohepatitis. Gastroenterology 2017; 152:1449-1461.e7. [PMID: 28132890 PMCID: PMC5406239 DOI: 10.1053/j.gastro.2017.01.015] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [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: 03/02/2016] [Revised: 12/21/2016] [Accepted: 01/09/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Nonalcoholic fatty liver disease (NAFLD) is a consequence of defects in diverse metabolic pathways that involve hepatic accumulation of triglycerides. Features of these aberrations might determine whether NAFLD progresses to nonalcoholic steatohepatitis (NASH). We investigated whether the diverse defects observed in patients with NAFLD are caused by different NAFLD subtypes with specific serum metabolomic profiles, and whether these can distinguish patients with NASH from patients with simple steatosis. METHODS We collected liver and serum from methionine adenosyltransferase 1a knockout (MAT1A-KO) mice, which have chronically low levels of hepatic S-adenosylmethionine (SAMe) and spontaneously develop steatohepatitis, as well as C57Bl/6 mice (controls); the metabolomes of all samples were determined. We also analyzed serum metabolomes of 535 patients with biopsy-proven NAFLD (353 with simple steatosis and 182 with NASH) and compared them with serum metabolomes of mice. MAT1A-KO mice were also given SAMe (30 mg/kg/day for 8 weeks); liver samples were collected and analyzed histologically for steatohepatitis. RESULTS Livers of MAT1A-KO mice were characterized by high levels of triglycerides, diglycerides, fatty acids, ceramides, and oxidized fatty acids, as well as low levels of SAMe and downstream metabolites. There was a correlation between liver and serum metabolomes. We identified a serum metabolomic signature associated with MAT1A-KO mice that also was present in 49% of the patients; based on this signature, we identified 2 NAFLD subtypes. We identified specific panels of markers that could distinguish patients with NASH from patients with simple steatosis for each subtype of NAFLD. Administration of SAMe reduced features of steatohepatitis in MAT1A-KO mice. CONCLUSIONS In an analysis of serum metabolomes of patients with NAFLD and MAT1A-KO mice with steatohepatitis, we identified 2 major subtypes of NAFLD and markers that differentiate steatosis from NASH in each subtype. These might be used to monitor disease progression and identify therapeutic targets for patients.
Collapse
Affiliation(s)
- Cristina Alonso
- OWL Metabolomics, Parque Tecnológico de Bizkaia, Derio,
Spain
| | | | - Marta Varela-Rey
- CIC bioGUNE, CIBERehd, Parque Tecnológico de Bizkaia, Derio,
Spain
| | | | - Nicolás Navasa
- CIC bioGUNE, CIBERehd, Parque Tecnológico de Bizkaia, Derio,
Spain
| | | | - José L Lavin
- CIC bioGUNE, CIBERehd, Parque Tecnológico de Bizkaia, Derio,
Spain
| | - Rebeca Mayo
- OWL Metabolomics, Parque Tecnológico de Bizkaia, Derio,
Spain
| | | | | | | | | | - Itziar Mincholé
- OWL Metabolomics, Parque Tecnológico de Bizkaia, Derio,
Spain
| | - Aaron Robinson
- Advanced Clinical Biosystems Research Institute, Cedars-Sinai
Medical Center, Los Angeles, CA, USA
| | - Javier Crespo
- Gastroenterology and Hepatology Department. Infection, Immunity and
Digestive Pathology Group. IDIVAL, Instituto de Investigación Valdecilla.
Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Antonio Martín-Duce
- Hospital Universitario Príncipe de Asturias. Faculty of
Medicine and Health Science. Alcalá University, Madrid, Spain
| | - Manuel Romero-Gomez
- Unidad de Enfermedades Digestivas. Hospital Virgen de Valme.
Hospital Universitario Virgen Macarena y Virgen del Rocío. Instituto de
Biomedicina de Sevilla, Universidad de Sevilla, CIBERehd, Seville, Spain
| | - Holger Sann
- Abbott Laboratories GmbH, Freundallee 9A, 30173 Hannover,
Germany
| | - Julian Platon
- Abbott, Hegenheimermattweg 127, 4123 Allschwil, Switzerland
| | - Jennifer Van Eyk
- Advanced Clinical Biosystems Research Institute, Cedars-Sinai
Medical Center, Los Angeles, CA, USA
| | - Patricia Aspichueta
- Department of Physiology, University of the Basque Country,
Biocruces Research Institute, Spain
| | - Mazen Noureddin
- Division of Digestive and Liver Diseases, Cedars-Sinai Medical
Center, Los Angeles, CA, USA
| | | | - Juan Anguita
- CIC bioGUNE, CIBERehd, Parque Tecnológico de Bizkaia, Derio,
Spain
| | - Ana M Aransay
- CIC bioGUNE, CIBERehd, Parque Tecnológico de Bizkaia, Derio,
Spain
| | | | - Shelly C Lu
- Division of Digestive and Liver Diseases, Cedars-Sinai Medical
Center, Los Angeles, CA, USA
| | - José M Mato
- CIC bioGUNE, CIBERehd, Parque Tecnológico de Bizkaia, Derio, Spain.
| |
Collapse
|
42
|
Lavín JL, Sánchez-Morán M, Bárcena L, Cortazar AR, Macías-Cámara N, González M, Aransay AM. A fistful of tips for a fruitful high throughput sequencing experiment. Bioessays 2017; 39. [PMID: 28378933 DOI: 10.1002/bies.201700037] [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] [Indexed: 11/09/2022]
Affiliation(s)
- José L Lavín
- Genome Analysis Platform, CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, Spain
| | - Mirian Sánchez-Morán
- Genome Analysis Platform, CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, Spain
| | - Laura Bárcena
- Genome Analysis Platform, CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, Spain
| | - Ana R Cortazar
- Genome Analysis Platform, CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, Spain
| | - Nuria Macías-Cámara
- Genome Analysis Platform, CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, Spain
| | - Monika González
- Genome Analysis Platform, CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, Spain
| | - Ana M Aransay
- Genome Analysis Platform, CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), ISCIII, Madrid, Spain
| |
Collapse
|
43
|
Suarez-Álvarez B, Rodríguez RM, Schlangen K, Raneros AB, Márquez-Kisinousky L, Fernández AF, Díaz-Corte C, Aransay AM, López-Larrea C. Phenotypic characteristics of aged CD4 + CD28 null T lymphocytes are determined by changes in the whole-genome DNA methylation pattern. Aging Cell 2017; 16:293-303. [PMID: 28026094 PMCID: PMC5334526 DOI: 10.1111/acel.12552] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [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] [Accepted: 10/31/2016] [Indexed: 01/01/2023] Open
Abstract
Aging is associated with a progressive loss of the CD28 costimulatory molecule in CD4+ lymphocytes (CD28null T cells), which is accompanied by the acquisition of new biological and functional properties that give rise to an impaired immune response. The regulatory mechanisms that govern the appearance and function of this cell subset during aging and in several associated inflammatory disorders remain controversial. Here, we present the whole‐genome DNA methylation and gene expression profiles of CD28null T cells and its CD28+ counterpart. A comparative analysis revealed that 296 genes are differentially methylated between the two cell subsets. A total of 160 genes associated with cytotoxicity (e.g. GRZB,TYROBP, and RUNX3) and cytokine/chemokine signaling (e.g. CX3CR1,CD27, and IL‐1R) are demethylated in CD28null T cells, while 136 de novo‐methylated genes matched defects in the TCR signaling pathway (e.g. ITK,TXK,CD3G, and LCK). TCR‐landscape analysis confirmed that CD28null T cells have an oligo/monoclonal expansion over the polyclonal background of CD28+ T cells, but feature a Vβ family repertoire specific to each individual. We reported that CD28null T cells show a preactivation state characterized by a higher level of expression of inflammasome‐related genes that leads to the release of IL‐1β when activated. Overall, our results demonstrate that CD28null T cells have a unique DNA methylation landscape, which is associated with differences in gene expression, contributing to the functionality of these cells. Understanding these epigenetic regulatory mechanisms could suggest novel therapeutic strategies to prevent the accumulation and activation of these cells during aging.
Collapse
Affiliation(s)
| | - Ramón M. Rodríguez
- Department of Immunology; Hospital Universitario Central de Asturias; Oviedo Spain
| | - Karin Schlangen
- Genome Analysis Platform; CIC bioGUNE; Bizkaia Technological Technology Park; Derio Spain
| | | | | | - Agustín F. Fernández
- Cancer Epigenetics Laboratory; Institute of Oncology of Asturias (IUOPA); Hospital Universitario Central de Asturias; Oviedo Spain
| | - Carmen Díaz-Corte
- Department of Nephrology; Hospital Universitario Central de Asturias; Oviedo Spain
| | - Ana M. Aransay
- Genome Analysis Platform; CIC bioGUNE; Bizkaia Technological Technology Park; Derio Spain
- CIBERhed
| | - Carlos López-Larrea
- Department of Immunology; Hospital Universitario Central de Asturias; Oviedo Spain
| |
Collapse
|
44
|
Rodriguez RM, Suarez-Alvarez B, Lavín JL, Mosén-Ansorena D, Baragaño Raneros A, Márquez-Kisinousky L, Aransay AM, Lopez-Larrea C. Epigenetic Networks Regulate the Transcriptional Program in Memory and Terminally Differentiated CD8+ T Cells. J Immunol 2016; 198:937-949. [PMID: 27974453 DOI: 10.4049/jimmunol.1601102] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 11/13/2016] [Indexed: 12/12/2022]
Abstract
Epigenetic mechanisms play a critical role during differentiation of T cells by contributing to the formation of stable and heritable transcriptional patterns. To better understand the mechanisms of memory maintenance in CD8+ T cells, we performed genome-wide analysis of DNA methylation, histone marking (acetylated lysine 9 in histone H3 and trimethylated lysine 9 in histone), and gene-expression profiles in naive, effector memory (EM), and terminally differentiated EM (TEMRA) cells. Our results indicate that DNA demethylation and histone acetylation are coordinated to generate the transcriptional program associated with memory cells. Conversely, EM and TEMRA cells share a very similar epigenetic landscape. Nonetheless, the TEMRA transcriptional program predicts an innate immunity phenotype associated with genes never reported in these cells, including several mediators of NK cell activation (VAV3 and LYN) and a large array of NK receptors (e.g., KIR2DL3, KIR2DL4, KIR2DL1, KIR3DL1, KIR2DS5). In addition, we identified up to 161 genes that encode transcriptional regulators, some of unknown function in CD8+ T cells, and that were differentially expressed in the course of differentiation. Overall, these results provide new insights into the regulatory networks involved in memory CD8+ T cell maintenance and T cell terminal differentiation.
Collapse
Affiliation(s)
- Ramon M Rodriguez
- Department of Immunology, Central University Hospital of Asturias, 33011 Oviedo, Spain
| | | | - José L Lavín
- Genome Analysis Platform, CIC bioGUNE and CIBERehd, Technological Park of Bizkaia, 48160 Derio, Spain
| | - David Mosén-Ansorena
- Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215; and
| | - Aroa Baragaño Raneros
- Department of Immunology, Central University Hospital of Asturias, 33011 Oviedo, Spain
| | | | - Ana M Aransay
- Genome Analysis Platform, CIC bioGUNE and CIBERehd, Technological Park of Bizkaia, 48160 Derio, Spain
| | - Carlos Lopez-Larrea
- Department of Immunology, Central University Hospital of Asturias, 33011 Oviedo, Spain; .,Fundación Renal Íñigo Álvarez de Toledo, 28003 Madrid, Spain
| |
Collapse
|
45
|
Martín-Martín N, Piva M, Urosevic J, Aldaz P, Sutherland JD, Fernández-Ruiz S, Arreal L, Torrano V, Cortazar AR, Planet E, Guiu M, Radosevic-Robin N, Garcia S, Macías I, Salvador F, Domenici G, Rueda OM, Zabala-Letona A, Arruabarrena-Aristorena A, Zúñiga-García P, Caro-Maldonado A, Valcárcel-Jiménez L, Sánchez-Mosquera P, Varela-Rey M, Martínez-Chantar ML, Anguita J, Ibrahim YH, Scaltriti M, Lawrie CH, Aransay AM, Iovanna JL, Baselga J, Caldas C, Barrio R, Serra V, dM Vivanco M, Matheu A, Gomis RR, Carracedo A. Stratification and therapeutic potential of PML in metastatic breast cancer. Nat Commun 2016; 7:12595. [PMID: 27553708 PMCID: PMC4999521 DOI: 10.1038/ncomms12595] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 07/12/2016] [Indexed: 01/15/2023] Open
Abstract
Patient stratification has been instrumental for the success of targeted therapies in breast cancer. However, the molecular basis of metastatic breast cancer and its therapeutic vulnerabilities remain poorly understood. Here we show that PML is a novel target in aggressive breast cancer. The acquisition of aggressiveness and metastatic features in breast tumours is accompanied by the elevated PML expression and enhanced sensitivity to its inhibition. Interestingly, we find that STAT3 is responsible, at least in part, for the transcriptional upregulation of PML in breast cancer. Moreover, PML targeting hampers breast cancer initiation and metastatic seeding. Mechanistically, this biological activity relies on the regulation of the stem cell gene SOX9 through interaction of PML with its promoter region. Altogether, we identify a novel pathway sustaining breast cancer aggressiveness that can be therapeutically exploited in combination with PML-based stratification.
Collapse
Affiliation(s)
| | - Marco Piva
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
| | - Jelena Urosevic
- Oncology Programme, Institute for Research in Biomedicine (IRB-Barcelona), 08028 Barcelona, Spain
| | - Paula Aldaz
- Oncology Area, Biodonostia Institute, 20014 San Sebastian, Spain
| | | | | | - Leire Arreal
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
| | - Verónica Torrano
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
| | - Ana R. Cortazar
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
| | - Evarist Planet
- Biostatistics and Bioinformatics Unit, Institute for Research in Biomedicine (IRB-Barcelona), 08028 Barcelona, Spain
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Marc Guiu
- Oncology Programme, Institute for Research in Biomedicine (IRB-Barcelona), 08028 Barcelona, Spain
| | - Nina Radosevic-Robin
- ERTICa Research Group, University of Auvergne EA4677, Clermont-Ferrand, France
- Biodiagnostics Laboratory OncoGenAuvergne, Pathology Unit, Jean Perrin Comprehensive Cancer Center, 63000 Clermont-Ferrand, France
| | - Stephane Garcia
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM UMR 1068, CNRS UMR 7258, Aix-Marseille University and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
| | - Iratxe Macías
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
| | - Fernando Salvador
- Oncology Programme, Institute for Research in Biomedicine (IRB-Barcelona), 08028 Barcelona, Spain
| | - Giacomo Domenici
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
| | - Oscar M. Rueda
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | | | | | | | | | | | | | - Marta Varela-Rey
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)
| | - Maria Luz Martínez-Chantar
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)
| | - Juan Anguita
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
- IKERBASQUE, Basque foundation for science, 48013 Bilbao, Spain
| | - Yasir H. Ibrahim
- Experimental Therapeutics Group, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
- Weill Cornell Medicine, New York 10021, USA
| | - Maurizio Scaltriti
- Human Oncology and Pathogenesis Program, Department of Pathology, Memorial Sloan-Kettering Cancer Center, 10065 New York, USA
| | - Charles H. Lawrie
- Oncology Area, Biodonostia Institute, 20014 San Sebastian, Spain
- IKERBASQUE, Basque foundation for science, 48013 Bilbao, Spain
| | - Ana M. Aransay
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)
| | - Juan L. Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM UMR 1068, CNRS UMR 7258, Aix-Marseille University and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
| | - Jose Baselga
- Human Oncology and Pathogenesis Program, Department of Medicine, Memorial Sloan-Kettering Cancer Center, 10065 New York, USA
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Rosa Barrio
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
| | - Maria dM Vivanco
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
| | - Ander Matheu
- Oncology Area, Biodonostia Institute, 20014 San Sebastian, Spain
- IKERBASQUE, Basque foundation for science, 48013 Bilbao, Spain
| | - Roger R. Gomis
- Oncology Programme, Institute for Research in Biomedicine (IRB-Barcelona), 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Arkaitz Carracedo
- CIC bioGUNE, Bizkaia Technology Park, Bulding 801a, 48160 Derio, Spain
- IKERBASQUE, Basque foundation for science, 48013 Bilbao, Spain
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), 48949 Leioa, Spain
| |
Collapse
|
46
|
Gomez-Sanchez JA, Carty L, Iruarrizaga-Lejarreta M, Palomo-Irigoyen M, Varela-Rey M, Griffith M, Hantke J, Macias-Camara N, Azkargorta M, Aurrekoetxea I, De Juan VG, Jefferies HBJ, Aspichueta P, Elortza F, Aransay AM, Martínez-Chantar ML, Baas F, Mato JM, Mirsky R, Woodhoo A, Jessen KR. Schwann cell autophagy, myelinophagy, initiates myelin clearance from injured nerves. J Cell Biol 2015; 210:153-68. [PMID: 26150392 PMCID: PMC4494002 DOI: 10.1083/jcb.201503019] [Citation(s) in RCA: 283] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 06/03/2015] [Indexed: 02/07/2023] Open
Abstract
Although Schwann cell myelin breakdown is the universal outcome of a remarkably wide range of conditions that cause disease or injury to peripheral nerves, the cellular and molecular mechanisms that make Schwann cell-mediated myelin digestion possible have not been established. We report that Schwann cells degrade myelin after injury by a novel form of selective autophagy, myelinophagy. Autophagy was up-regulated by myelinating Schwann cells after nerve injury, myelin debris was present in autophagosomes, and pharmacological and genetic inhibition of autophagy impaired myelin clearance. Myelinophagy was positively regulated by the Schwann cell JNK/c-Jun pathway, a central regulator of the Schwann cell reprogramming induced by nerve injury. We also present evidence that myelinophagy is defective in the injured central nervous system. These results reveal an important role for inductive autophagy during Wallerian degeneration, and point to potential mechanistic targets for accelerating myelin clearance and improving demyelinating disease.
Collapse
Affiliation(s)
- Jose A Gomez-Sanchez
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, England, UK
| | - Lucy Carty
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, England, UK
| | - Marta Iruarrizaga-Lejarreta
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Bizkaia, Spain
| | - Marta Palomo-Irigoyen
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Bizkaia, Spain
| | - Marta Varela-Rey
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Bizkaia, Spain
| | - Megan Griffith
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, England, UK
| | - Janina Hantke
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, England, UK
| | - Nuria Macias-Camara
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Bizkaia, Spain
| | - Mikel Azkargorta
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Bizkaia, Spain ProteoRed-ISCIII
| | - Igor Aurrekoetxea
- Department of Physiology, Faculty of Medicine and Dentistry, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain Biocruces Health Research Institute, 48903 Barakaldo, Spain
| | - Virginia Gutiérrez De Juan
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Bizkaia, Spain
| | - Harold B J Jefferies
- The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, England, UK
| | - Patricia Aspichueta
- Department of Physiology, Faculty of Medicine and Dentistry, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain Biocruces Health Research Institute, 48903 Barakaldo, Spain
| | - Félix Elortza
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Bizkaia, Spain ProteoRed-ISCIII
| | - Ana M Aransay
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Bizkaia, Spain
| | - María L Martínez-Chantar
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Bizkaia, Spain Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), E-48080 Bilbao, Spain
| | - Frank Baas
- Department of Genome Analysis, Academic Medical Centre, 1105 AZ Amsterdam, Netherlands
| | - José M Mato
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Bizkaia, Spain
| | - Rhona Mirsky
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, England, UK
| | - Ashwin Woodhoo
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Bizkaia, Spain Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Kristján R Jessen
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, England, UK
| |
Collapse
|
47
|
Ugalde-Olano A, Egia A, Fernández-Ruiz S, Loizaga-Iriarte A, Zuñiga-García P, Garcia S, Royo F, Lacasa-Viscasillas I, Castro E, Cortazar AR, Zabala-Letona A, Martín-Martín N, Arruabarrena-Aristorena A, Torrano-Moya V, Valcárcel-Jiménez L, Sánchez-Mosquera P, Caro-Maldonado A, González-Tampan J, Cachi-Fuentes G, Bilbao E, Montero R, Fernández S, Arrieta E, Zorroza K, Castillo-Martín M, Serra V, Salazar E, Macías-Cámara N, Tabernero J, Baselga J, Cordón-Cardo C, Aransay AM, Villar AD, Iovanna JL, Falcón-Pérez JM, Unda M, Bilbao R, Carracedo A. Methodological aspects of the molecular and histological study of prostate cancer: focus on PTEN. Methods 2015; 77-78:25-30. [PMID: 25697760 PMCID: PMC4503808 DOI: 10.1016/j.ymeth.2015.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 12/31/2022] Open
Abstract
Prostate cancer is among the most frequent cancers in men, and despite its high rate of cure, the high number of cases results in an elevated mortality worldwide. Importantly, prostate cancer incidence is dramatically increasing in western societies in the past decades, suggesting that this type of tumor is exquisitely sensitive to lifestyle changes. Prostate cancer frequently exhibits alterations in the PTEN gene (inactivating mutations or gene deletions) or at the protein level (reduced protein expression or altered sub-cellular compartmentalization). The relevance of PTEN in this type of cancer is further supported by the fact that the sole deletion of PTEN in the murine prostate epithelium recapitulates many of the features of the human disease. In order to study the molecular alterations in prostate cancer, we need to overcome the methodological challenges that this tissue imposes. In this review we present protocols and methods, using PTEN as proof of concept, to study different molecular characteristics of prostate cancer.
Collapse
Affiliation(s)
| | - Ainara Egia
- Basque Biobank, Basque Foundation for Health Innovation and Research-BIOEF, Barakaldo, Spain
| | | | | | | | - Stephane Garcia
- Centre de Recherche en Carcérologie de Marseille (CRCM), INSERM UMR 1068, CNRS UMR 7258, Aix-Marseille University and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Félix Royo
- CIC bioGUNE, Bizkaia Technology Park, 801 Building, 48160 Derio, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Spain
| | | | - Erika Castro
- Basque Biobank, Basque Foundation for Health Innovation and Research-BIOEF, Barakaldo, Spain
| | - Ana R Cortazar
- CIC bioGUNE, Bizkaia Technology Park, 801 Building, 48160 Derio, Spain
| | | | | | | | | | | | | | | | | | | | - Elena Bilbao
- Department of Urology, Basurto University Hospital, 48013 Bilbao, Spain
| | - Rocío Montero
- Department of Urology, Basurto University Hospital, 48013 Bilbao, Spain
| | - Sara Fernández
- Department of Pathology, Basurto University Hospital, 48013 Bilbao, Spain; Basque Biobank, Basque Foundation for Health Innovation and Research-BIOEF, Barakaldo, Spain
| | - Edurne Arrieta
- Basque Biobank, Basque Foundation for Health Innovation and Research-BIOEF, Barakaldo, Spain
| | - Kerman Zorroza
- Basque Biobank, Basque Foundation for Health Innovation and Research-BIOEF, Barakaldo, Spain
| | | | - Violeta Serra
- Molecular Therapeutics Research Unit, Medical Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain; Experimental Therapeutics Group, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Eider Salazar
- Basque Biobank, Basque Foundation for Health Innovation and Research-BIOEF, Barakaldo, Spain
| | | | - Jose Tabernero
- Molecular Therapeutics Research Unit, Medical Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain; Experimental Therapeutics Group, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Jose Baselga
- Molecular Therapeutics Research Unit, Medical Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain; Experimental Therapeutics Group, Vall d'Hebron University Hospital, Barcelona, Spain; Human Oncology & Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Carlos Cordón-Cardo
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ana M Aransay
- CIC bioGUNE, Bizkaia Technology Park, 801 Building, 48160 Derio, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Spain
| | - Amaia Del Villar
- Basque Biobank, Basque Foundation for Health Innovation and Research-BIOEF, Barakaldo, Spain
| | - Juan L Iovanna
- Centre de Recherche en Carcérologie de Marseille (CRCM), INSERM UMR 1068, CNRS UMR 7258, Aix-Marseille University and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Juan M Falcón-Pérez
- CIC bioGUNE, Bizkaia Technology Park, 801 Building, 48160 Derio, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Miguel Unda
- Department of Urology, Basurto University Hospital, 48013 Bilbao, Spain
| | - Roberto Bilbao
- Basque Biobank, Basque Foundation for Health Innovation and Research-BIOEF, Barakaldo, Spain
| | - Arkaitz Carracedo
- CIC bioGUNE, Bizkaia Technology Park, 801 Building, 48160 Derio, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain; Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), Bilbao, Spain.
| |
Collapse
|
48
|
Salazar M, Lorente M, García-Taboada E, Gómez EP, Dávila D, Zúñiga-García P, Flores JM, Rodríguez A, Hegedus Z, Mosén-Ansorena D, Aransay AM, Hernández-Tiedra S, López-Valero I, Quintanilla M, Sánchez C, Iovanna JL, Dusetti N, Guzmán M, Francis SE, Carracedo A, Kiss-Toth E, Velasco G. TRIB3 suppresses tumorigenesis by controlling mTORC2/AKT/FOXO signaling. Mol Cell Oncol 2015; 2:e980134. [PMID: 27308456 PMCID: PMC4905291 DOI: 10.4161/23723556.2014.980134] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 10/20/2014] [Accepted: 10/21/2014] [Indexed: 11/19/2022]
Abstract
In a recent article, we found that Tribbles pseudokinase 3 (TRIB3) plays a tumor suppressor role and that this effect relies on the dysregulation of the phosphorylation of v-akt murine thymoma viral oncogene homolog (AKT) by the mammalian target of rapamycin complex 2 (mTORC2 complex), and the subsequent hyperphosphorylation and inactivation of the transcription factor Forkhead box O3 (FOXO3).
Collapse
Affiliation(s)
- María Salazar
- Department of Biochemistry and Molecular Biology I; School of Biology; Complutense University; Madrid, Spain; Instituto de Investigaciones Sanitarias San Carlos (IdISSC); Madrid, Spain
| | - Mar Lorente
- Department of Biochemistry and Molecular Biology I; School of Biology; Complutense University; Madrid, Spain; Instituto de Investigaciones Sanitarias San Carlos (IdISSC); Madrid, Spain
| | - Elena García-Taboada
- Department of Biochemistry and Molecular Biology I; School of Biology; Complutense University ; Madrid, Spain
| | - Eduardo Pérez Gómez
- Department of Biochemistry and Molecular Biology I; School of Biology; Complutense University; Madrid, Spain; Instituto de Investigación Hospital 12 de Octubre (I+12); Madrid, Spain
| | - David Dávila
- Department of Biochemistry and Molecular Biology I; School of Biology; Complutense University; Madrid, Spain; Instituto de Investigaciones Sanitarias San Carlos (IdISSC); Madrid, Spain
| | | | - Juana M Flores
- Department of Animal Surgery and Medicine; School of Veterinary; Complutense University ; Madrid, Spain
| | - Antonio Rodríguez
- Department of Animal Surgery and Medicine; School of Veterinary; Complutense University ; Madrid, Spain
| | - Zoltan Hegedus
- Institute of Biophysics; Hungarian Academy of Sciences ; Szeged, Hungary
| | | | - Ana M Aransay
- CIC bioGUNE-CIBERehd, Bizkaia Technology Park ; Derio, Spain
| | - Sonia Hernández-Tiedra
- Department of Biochemistry and Molecular Biology I; School of Biology; Complutense University; Madrid, Spain; Instituto de Investigaciones Sanitarias San Carlos (IdISSC); Madrid, Spain
| | - Israel López-Valero
- Department of Biochemistry and Molecular Biology I; School of Biology; Complutense University; Madrid, Spain; Instituto de Investigaciones Sanitarias San Carlos (IdISSC); Madrid, Spain
| | - Miguel Quintanilla
- Instituto de Investigaciones Biomédicas Alberto Sols; Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM) ; Madrid, Spain
| | - Cristina Sánchez
- Department of Biochemistry and Molecular Biology I; School of Biology; Complutense University; Madrid, Spain; Instituto de Investigación Hospital 12 de Octubre (I+12); Madrid, Spain
| | - Juan L Iovanna
- Centre de Recherche en Carcérologie de Marseille (CRCM); INSERM UMR 1068, CNRS UMR 7258, Aix Marseille Université and Institut Paoli Calmette ; Marseille, France
| | - Nelson Dusetti
- Centre de Recherche en Carcérologie de Marseille (CRCM); INSERM UMR 1068, CNRS UMR 7258, Aix Marseille Université and Institut Paoli Calmette ; Marseille, France
| | - Manuel Guzmán
- Department of Biochemistry and Molecular Biology I; School of Biology; Complutense University; Madrid, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED) and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS); Madrid, Spain
| | - Sheila E Francis
- Department of Cardiovascular Science; University of Sheffield ; Sheffield, UK
| | - Arkaitz Carracedo
- CIC bioGUNE, Bizkaia Technology Park; Derio, Spain; Ikerbasque, Basque Foundation for Science; Bilbao, Spain; Biochemistry and Molecular Biology Department; University of the Basque Country (UPV/EHU); Bilbao, Spain
| | - Endre Kiss-Toth
- Department of Cardiovascular Science; University of Sheffield ; Sheffield, UK
| | - Guillermo Velasco
- Department of Biochemistry and Molecular Biology I; School of Biology; Complutense University; Madrid, Spain; Instituto de Investigaciones Sanitarias San Carlos (IdISSC); Madrid, Spain
| |
Collapse
|
49
|
Rodriguez RM, Suarez-Alvarez B, Mosén-Ansorena D, García-Peydró M, Fuentes P, García-León MJ, Gonzalez-Lahera A, Macias-Camara N, Toribio ML, Aransay AM, Lopez-Larrea C. Regulation of the transcriptional program by DNA methylation during human αβ T-cell development. Nucleic Acids Res 2014; 43:760-74. [PMID: 25539926 PMCID: PMC4333391 DOI: 10.1093/nar/gku1340] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Thymocyte differentiation is a complex process involving well-defined sequential developmental stages that ultimately result in the generation of mature T-cells. In this study, we analyzed DNA methylation and gene expression profiles at successive human thymus developmental stages. Gain and loss of methylation occurred during thymocyte differentiation, but DNA demethylation was much more frequent than de novo methylation and more strongly correlated with gene expression. These changes took place in CpG-poor regions and were closely associated with T-cell differentiation and TCR function. Up to 88 genes that encode transcriptional regulators, some of whose functions in T-cell development are as yet unknown, were differentially methylated during differentiation. Interestingly, no reversion of accumulated DNA methylation changes was observed as differentiation progressed, except in a very small subset of key genes (RAG1, RAG2, CD8A, PTCRA, etc.), indicating that methylation changes are mostly unique and irreversible events. Our study explores the contribution of DNA methylation to T-cell lymphopoiesis and provides a fine-scale map of differentially methylated regions associated with gene expression changes. These can lay the molecular foundations for a better interpretation of the regulatory networks driving human thymopoiesis.
Collapse
Affiliation(s)
- Ramon M Rodriguez
- Department of Immunology, Hospital Universitario Central de Asturias, 33006 Oviedo, Spain
| | - Beatriz Suarez-Alvarez
- Cellular Biology in Renal Diseases Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - David Mosén-Ansorena
- Genome Analysis Platform, CIC bioGUNE & CIBERehd, Technological Park of Bizkaia - Building 801A, 48160 Derio, Spain
| | - Marina García-Peydró
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Patricia Fuentes
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - María J García-León
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Aintzane Gonzalez-Lahera
- Genome Analysis Platform, CIC bioGUNE & CIBERehd, Technological Park of Bizkaia - Building 801A, 48160 Derio, Spain
| | - Nuria Macias-Camara
- Genome Analysis Platform, CIC bioGUNE & CIBERehd, Technological Park of Bizkaia - Building 801A, 48160 Derio, Spain
| | - María L Toribio
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Ana M Aransay
- Genome Analysis Platform, CIC bioGUNE & CIBERehd, Technological Park of Bizkaia - Building 801A, 48160 Derio, Spain
| | - Carlos Lopez-Larrea
- Department of Immunology, Hospital Universitario Central de Asturias, 33006 Oviedo, Spain Fundación Renal 'Íñigo Álvarez de Toledo', 28003 Madrid, Spain
| |
Collapse
|
50
|
Salazar M, Lorente M, García-Taboada E, Pérez Gómez E, Dávila D, Zúñiga-García P, María Flores J, Rodríguez A, Hegedus Z, Mosén-Ansorena D, Aransay AM, Hernández-Tiedra S, López-Valero I, Quintanilla M, Sánchez C, Iovanna JL, Dusetti N, Guzmán M, Francis SE, Carracedo A, Kiss-Toth E, Velasco G. Loss of Tribbles pseudokinase-3 promotes Akt-driven tumorigenesis via FOXO inactivation. Cell Death Differ 2014; 22:131-44. [PMID: 25168244 DOI: 10.1038/cdd.2014.133] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 07/11/2014] [Accepted: 07/24/2014] [Indexed: 01/08/2023] Open
Abstract
Tribbles pseudokinase-3 (TRIB3) has been proposed to act as an inhibitor of AKT although the precise molecular basis of this activity and whether the loss of TRIB3 contributes to cancer initiation and progression remain to be clarified. In this study, by using a wide array of in vitro and in vivo approaches, including a Trib3 knockout mouse, we demonstrate that TRIB3 has a tumor-suppressing role. We also find that the mechanism by which TRIB3 loss enhances tumorigenesis relies on the dysregulation of the phosphorylation of AKT by the mTORC2 complex, which leads to an enhanced phosphorylation of AKT on Ser473 and the subsequent hyperphosphorylation and inactivation of the transcription factor FOXO3. These observations support the notion that loss of TRIB3 is associated with a more aggressive phenotype in various types of tumors by enhancing the activity of the mTORC2/AKT/FOXO axis.
Collapse
Affiliation(s)
- M Salazar
- 1] Department of Biochemistry and Molecular Biology I, School of Biology, Complutense University, Madrid, Spain [2] Instituto de Investigaciones Sanitarias San Carlos (IdISSC), Madrid, Spain
| | - M Lorente
- 1] Department of Biochemistry and Molecular Biology I, School of Biology, Complutense University, Madrid, Spain [2] Instituto de Investigaciones Sanitarias San Carlos (IdISSC), Madrid, Spain
| | - E García-Taboada
- Department of Biochemistry and Molecular Biology I, School of Biology, Complutense University, Madrid, Spain
| | - E Pérez Gómez
- 1] Department of Biochemistry and Molecular Biology I, School of Biology, Complutense University, Madrid, Spain [2] Instituto de Investigación Hospital 12 de Octubre (I+12), Madrid, Spain
| | - D Dávila
- 1] Department of Biochemistry and Molecular Biology I, School of Biology, Complutense University, Madrid, Spain [2] Instituto de Investigaciones Sanitarias San Carlos (IdISSC), Madrid, Spain
| | | | - J María Flores
- Department of Animal Surgery and Medicine, School of Veterinary, Complutense University, Madrid, Spain
| | - A Rodríguez
- Department of Animal Surgery and Medicine, School of Veterinary, Complutense University, Madrid, Spain
| | - Z Hegedus
- Institute of Biophysics, Hungarian Academy of Sciences, Szeged, Hungary
| | | | - A M Aransay
- CIC bioGUNE-CIBERehd, Bizkaia Technology Park, Derio, Spain
| | - S Hernández-Tiedra
- 1] Department of Biochemistry and Molecular Biology I, School of Biology, Complutense University, Madrid, Spain [2] Instituto de Investigaciones Sanitarias San Carlos (IdISSC), Madrid, Spain
| | - I López-Valero
- 1] Department of Biochemistry and Molecular Biology I, School of Biology, Complutense University, Madrid, Spain [2] Instituto de Investigaciones Sanitarias San Carlos (IdISSC), Madrid, Spain
| | - M Quintanilla
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
| | - C Sánchez
- 1] Department of Biochemistry and Molecular Biology I, School of Biology, Complutense University, Madrid, Spain [2] Instituto de Investigación Hospital 12 de Octubre (I+12), Madrid, Spain
| | - J L Iovanna
- Centre de Recherche en Carcérologie de Marseille (CRCM), INSERM UMR, CNRS UMR 7258, Aix Marseille Université and Institut Paoli Calmette, Marseille, France
| | - N Dusetti
- Centre de Recherche en Carcérologie de Marseille (CRCM), INSERM UMR, CNRS UMR 7258, Aix Marseille Université and Institut Paoli Calmette, Marseille, France
| | - M Guzmán
- 1] Department of Biochemistry and Molecular Biology I, School of Biology, Complutense University, Madrid, Spain [2] Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED) and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, Spain
| | - S E Francis
- Department of Cardiovascular Science, University of Sheffield, Sheffield, UK
| | - A Carracedo
- 1] CIC bioGUNE, Bizkaia Technology Park, Derio, Spain [2] Ikerbasque, Basque Foundation for Science, Bilbao, Spain [3] Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - E Kiss-Toth
- Department of Cardiovascular Science, University of Sheffield, Sheffield, UK
| | - G Velasco
- 1] Department of Biochemistry and Molecular Biology I, School of Biology, Complutense University, Madrid, Spain [2] Instituto de Investigaciones Sanitarias San Carlos (IdISSC), Madrid, Spain
| |
Collapse
|