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Blanco-Doval A, Azkargorta M, Iloro I, Beaskoetxea J, Elortza F, Barron LJR, Aldai N. Comparative proteomic analysis of the changes in mare milk associated with different lactation stages and management systems. Food Chem 2024; 445:138766. [PMID: 38402663 DOI: 10.1016/j.foodchem.2024.138766] [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: 11/22/2023] [Revised: 01/24/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024]
Abstract
Mare milk has traditionally been attributed a number of health promoting properties. However, knowledge on its composition and functionality remains scarce, with particularly limited studies on mare milk proteomics. This study deeply characterized mare milk proteome accounting for both caseins and proteins in the whey fraction, also addressing the impact of lactation stage and different management systems. Milk samples from Basque Mountain Horse breed mares belonging to three different farms and three lactation stages were analysed after in-gel and in-solution digestion using nLC-MS/MS. Among the 469 proteins identified, the content of alpha-1 antitrypsin was significantly higher in pasture-based compared to other systems. Moreover, lactation stage significantly affected the content of beta-lactoglobulin II, immunoglobulin-like domain-containing protein, interferon alpha-inducible protein 27, lactotransferrin, polypeptide N-acetylgalactosaminyltransferase, and transforming acidic coiled-coil containing protein 2. This study contributes to the deep characterization of mare milk proteome and provides new insights into the effect of different production factors.
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Affiliation(s)
- Ana Blanco-Doval
- Lactiker Research Group, Department of Pharmacy and Food Sciences, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, Bizkaia Science and Technology Park, 48160 Derio, Spain.
| | - Ibon Iloro
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, Bizkaia Science and Technology Park, 48160 Derio, Spain.
| | - Jabier Beaskoetxea
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, Bizkaia Science and Technology Park, 48160 Derio, Spain.
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, Bizkaia Science and Technology Park, 48160 Derio, Spain.
| | - Luis Javier R Barron
- Lactiker Research Group, Department of Pharmacy and Food Sciences, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.
| | - Noelia Aldai
- Lactiker Research Group, Department of Pharmacy and Food Sciences, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.
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2
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Iruzubieta P, Damborenea A, Ioghen M, Bajew S, Fernandez-Torrón R, Töpf A, Herrero-Reiriz Á, Epure D, Vill K, Hernández-Laín A, Manterola M, Azkargorta M, Pikatza-Menoio O, Pérez-Fernandez L, García-Puga M, Gaina G, Bastian A, Streata I, Walter MC, Müller-Felber W, Thiele S, Moragón S, Bastida-Lertxundi N, López-Cortajarena A, Elortza F, Gereñu G, Alonso-Martin S, Straub V, de Sancho D, Teleanu R, López de Munain A, Blázquez L. Biallelic variants in SNUPN cause a limb girdle muscular dystrophy with myofibrillar-like features. Brain 2024:awae046. [PMID: 38366623 DOI: 10.1093/brain/awae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 01/20/2024] [Accepted: 01/28/2024] [Indexed: 02/18/2024] Open
Abstract
Alterations in RNA-splicing are a molecular hallmark of several neurological diseases, including muscular dystrophies where mutations in genes involved in RNA metabolism or characterised by alterations in RNA splicing have been described. Here, we present five patients from two unrelated families with a limb-girdle muscular dystrophy (LGMD) phenotype carrying a biallelic variant in SNUPN gene. Snurportin-1, the protein encoded by SNUPN, plays an important role in the nuclear transport of small nuclear ribonucleoproteins (snRNPs), essential components of the spliceosome. We combine deep phenotyping, including clinical features, histopathology and muscle magnetic resonance image (MRI), with functional studies in patient-derived cells and muscle biopsies to demonstrate that variants in SNUPN are the cause of a new type of LGMD according to current definition. Moreover, an in vivo model in Drosophila melanogaster further supports the relevance of Snurportin-1 in muscle. SNUPN patients show a similar phenotype characterised by proximal weakness starting in childhood, restrictive respiratory dysfunction and prominent contractures, although interindividual variability in terms of severity even in individuals from the same family was found. Muscle biopsy showed myofibrillar-like features consisting of myotilin deposits and Z-disc disorganisation. MRI showed predominant impairment of paravertebral, vasti, sartorius, gracilis, peroneal and medial gastrocnemius muscles. Conservation and structural analyses of Snurportin-1 p.Ile309Ser variant suggest an effect in nuclear-cytosol snRNP trafficking. In patient-derived fibroblasts and muscle, cytoplasmic accumulation of snRNP components is observed, while total expression of Snurportin-1 and snRNPs remains unchanged, which demonstrates a functional impact of SNUPN variant in snRNP metabolism. Furthermore, RNA-splicing analysis in patients' muscle showed widespread splicing deregulation, in particular in genes relevant for muscle development and splicing factors that participate in the early steps of spliceosome assembly. In conclusion, we report that SNUPN variants are a new cause of limb girdle muscular dystrophy with specific clinical, histopathological and imaging features, supporting SNUPN as a new gene to be included in genetic testing of myopathies. These results further support the relevance of splicing-related proteins in muscle disorders.
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Affiliation(s)
- Pablo Iruzubieta
- Department of Neurosciences, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
- Department of Neurology, Donostia University Hospital, Osakidetza Basque Health Service, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
| | - Alberto Damborenea
- Department of Neurosciences, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
| | - Mihaela Ioghen
- Clinical Neurosciences Department, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Paediatric Neurology, 020021 Bucharest, Romania
| | - Simon Bajew
- Department of Neurosciences, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
| | - Roberto Fernandez-Torrón
- Department of Neurosciences, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
- Department of Neurology, Donostia University Hospital, Osakidetza Basque Health Service, 20014 San Sebastián, Spain
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, NE4 5NR Newcastle Upon Tyne, UK
| | - Álvaro Herrero-Reiriz
- Department of Neurosciences, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
| | - Diana Epure
- Department of Paediatric Neurology, Doctor Victor Gomoiu Children's Hospital, 022102 Bucharest, Romania
| | - Katharina Vill
- Department of Pediatric Neurology and Developmental Medicine and LMU Center for Children with Medical Complexity, Dr. von Hauner Children's Hospital, LMU University Hospital, Ludwig-Maximilians-University Munich, 80539 Munich, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Aurelio Hernández-Laín
- Neuropathology Unit, Department of Pathology, 12 de Octubre University Hospital, 28041 Madrid, Spain
- Instituto de Investigación Sanitaria imas12, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
- Universidad Complutense de Madrid, Facultad de Medicina, 28040 Madrid, Spain
| | - María Manterola
- Department of Neurosciences, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain
- Centre for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Oihane Pikatza-Menoio
- Department of Neurosciences, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
| | - Laura Pérez-Fernandez
- Department of Neurosciences, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), 20014 San Sebastián, Spain
| | - Mikel García-Puga
- Department of Neurosciences, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
| | - Gisela Gaina
- Victor Babes National Institute of Pathology, 050096 Bucharest, Romania
| | - Alexandra Bastian
- Department of Pathology, Colentina Clinical Hospital, 020125 Bucharest, Romania
| | - Ioana Streata
- Human Genomics Laboratory, Regional Centre of Medical Genetics, Craiova University of Medicine and Pharmacy, 200349 Dolj, Romania
| | - Maggie C Walter
- Friedrich Baur Institute at the Department of Neurology, LMU University Hospital, Ludwig-Maximilians-University Munich, 80539 Munich, Germany
| | - Wolfgang Müller-Felber
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Simone Thiele
- Friedrich Baur Institute at the Department of Neurology, LMU University Hospital, Ludwig-Maximilians-University Munich, 80539 Munich, Germany
| | - Saioa Moragón
- Department of Neurosciences, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
| | - Nerea Bastida-Lertxundi
- Department of Clinical Genetics, Donostia University Hospital, Osakidetza Basque Health Service, 20014 San Sebastián, Spain
| | - Aitziber López-Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), 20014 San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain
- Centre for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Gorka Gereñu
- Department of Neurosciences, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Sonia Alonso-Martin
- Department of Neurosciences, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, NE4 5NR Newcastle Upon Tyne, UK
| | - David de Sancho
- Donostia International Physics Center, 20018 San Sebastián, Spain
- Faculty of Chemistry, University of the Basque Country, 20018 San Sebastián, Spain
| | - Raluca Teleanu
- Clinical Neurosciences Department, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Paediatric Neurology, 020021 Bucharest, Romania
| | - Adolfo López de Munain
- Department of Neurosciences, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
- Department of Neurology, Donostia University Hospital, Osakidetza Basque Health Service, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
- Faculty of Medicine, University of the Basque Country, 20014 San Sebastián, Spain
- Faculty of Medicine, University of Deusto, 48007 Bilbao, Spain
| | - Lorea Blázquez
- Department of Neurosciences, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), 28031, Madrid, Spain
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
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3
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Zeballos N, Comino N, Andrés-Sanz D, Santiago-Arcos J, Azkargorta M, Elortza F, Diamanti E, López-Gallego F. Region-Directed Enzyme Immobilization through Engineering Protein Surface with Histidine Clusters. ACS Appl Mater Interfaces 2024; 16:833-846. [PMID: 38135284 PMCID: PMC10788835 DOI: 10.1021/acsami.3c15993] [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] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
Enzyme immobilization is a key enabling technology for a myriad of industrial applications, yet immobilization science is still too empirical to reach highly active and robust heterogeneous biocatalysts through a general approach. Conventional protein immobilization methods lack control over how enzymes are oriented on solid carriers, resulting in negative conformational changes that drive enzyme deactivation. Site-selective enzyme immobilization through peptide tags and protein domains addresses the orientation issue, but this approach limits the possible orientations to the N- and C-termini of the target enzyme. In this work, we engineer the surface of two model dehydrogenases to introduce histidine clusters into flexible regions not involved in catalysis, through which immobilization is driven. By varying the position and the histidine density of the clusters, we create a small library of enzyme variants to be immobilized on different carriers functionalized with different densities of various metal chelates (Co2+, Cu2+, Ni2+, and Fe3+). We first demonstrate that His-clusters can be as efficient as the conventional His-tags in immobilizing enzymes, recovering even more activity and gaining stability against some denaturing agents. Furthermore, we find that the enzyme orientation as well as the type and density of the metal chelates affect the immobilization parameters (immobilization yield and recovered activity) and the stability of the immobilized enzymes. According to proteomic studies, His-clusters enable a different enzyme orientation as compared to His-tag. Finally, these oriented heterogeneous biocatalysts are implemented in batch reactions, demonstrating that the stability achieved by an optimized orientation translates into increased operational stability.
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Affiliation(s)
- Nicoll Zeballos
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
| | - Natalia Comino
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
| | - Daniel Andrés-Sanz
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
| | - Javier Santiago-Arcos
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
| | - Mikel Azkargorta
- Center
for Cooperative Research in Biology (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 800 Bld, 48160 Derio, Bizkaia, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Felix Elortza
- Center
for Cooperative Research in Biology (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 800 Bld, 48160 Derio, Bizkaia, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Eleftheria Diamanti
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
| | - Fernando López-Gallego
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
- Ikerbasque,
Basque Foundation for Science, 48013 Bilbao, Spain
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4
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Salgueiro V, Bertol J, Gutierrez C, Palacios A, Pasquina-Lemonche L, Espalliat A, Lerma L, Weinrick B, Lavin JL, Elortza F, Azkalgorta M, Prieto A, Buendía-Nacarino P, Luque-García JL, Neyrolles O, Cava F, Hobbs JK, Sanz J, Prados-Rosales R. Maintenance of cell wall remodeling and vesicle production are connected in Mycobacterium tuberculosis. bioRxiv 2023:2023.11.19.567727. [PMID: 38187572 PMCID: PMC10769192 DOI: 10.1101/2023.11.19.567727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Pathogenic and nonpathogenic mycobacteria secrete extracellular vesicles (EVs) under various conditions. EVs produced by Mycobacterium tuberculosis ( Mtb ) have raised significant interest for their potential in cell communication, nutrient acquisition, and immune evasion. However, the relevance of vesicle secretion during tuberculosis infection remains unknown due to the limited understanding of mycobacterial vesicle biogenesis. We have previously shown that a transposon mutant in the LCP-related gene virR ( virR mut ) manifested a strong attenuated phenotype during experimental macrophage and murine infections, concomitant to enhanced vesicle release. In this study, we aimed to understand the role of VirR in the vesicle production process in Mtb . We employ genetic, transcriptional, proteomics, ultrastructural and biochemical methods to investigate the underlying processes explaining the enhanced vesiculogenesis phenomenon observed in the virR mutant. Our results establish that VirR is critical to sustain proper cell permeability via regulation of cell envelope remodeling possibly through the interaction with similar cell envelope proteins, which control the link between peptidoglycan and arabinogalactan. These findings advance our understanding of mycobacterial extracellular vesicle biogenesis and suggest that these set of proteins could be attractive targets for therapeutic intervention.
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5
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Barroso-Gomila O, Merino-Cacho L, Muratore V, Perez C, Taibi V, Maspero E, Azkargorta M, Iloro I, Trulsson F, Vertegaal ACO, Mayor U, Elortza F, Polo S, Barrio R, Sutherland JD. BioE3 identifies specific substrates of ubiquitin E3 ligases. Nat Commun 2023; 14:7656. [PMID: 37996419 PMCID: PMC10667490 DOI: 10.1038/s41467-023-43326-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023] Open
Abstract
Hundreds of E3 ligases play a critical role in recognizing specific substrates for modification by ubiquitin (Ub). Separating genuine targets of E3s from E3-interactors remains a challenge. We present BioE3, a powerful approach for matching substrates to Ub E3 ligases of interest. Using BirA-E3 ligase fusions and bioUb, site-specific biotinylation of Ub-modified substrates of particular E3s facilitates proteomic identification. We show that BioE3 identifies both known and new targets of two RING-type E3 ligases: RNF4 (DNA damage response, PML bodies), and MIB1 (endocytosis, autophagy, centrosome dynamics). Versatile BioE3 identifies targets of an organelle-specific E3 (MARCH5) and a relatively uncharacterized E3 (RNF214). Furthermore, BioE3 works with NEDD4, a HECT-type E3, identifying new targets linked to vesicular trafficking. BioE3 detects altered specificity in response to chemicals, opening avenues for targeted protein degradation, and may be applicable for other Ub-likes (UbLs, e.g., SUMO) and E3 types. BioE3 applications shed light on cellular regulation by the complex UbL network.
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Affiliation(s)
- Orhi Barroso-Gomila
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Laura Merino-Cacho
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Veronica Muratore
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Coralia Perez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Vincenzo Taibi
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Elena Maspero
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Mikel Azkargorta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
- CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029, Madrid, Spain
| | - Ibon Iloro
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
- CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029, Madrid, Spain
| | - Fredrik Trulsson
- Cell and Chemical Biology, Leiden University Medical Center (LUMC), 2333, ZA, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Cell and Chemical Biology, Leiden University Medical Center (LUMC), 2333, ZA, Leiden, The Netherlands
| | - Ugo Mayor
- Ikerbasque, Basque Foundation for Science, 48011, Bilbao, Spain
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), E-48940, Leioa, Spain
| | - Felix Elortza
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
- CIBERehd, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029, Madrid, Spain
| | - Simona Polo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
- Dipartimento di oncologia ed emato-oncologia, Università degli Studi di Milano, Milan, Italy
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
| | - James D Sutherland
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
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6
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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.
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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.
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7
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Córdoba-Jover B, Ribera J, Portolés I, Lecue E, Rodriguez-Vita J, Pérez-Sisqués L, Mannara F, Solsona-Vilarrasa E, García-Ruiz C, Fernández-Checa JC, Casals G, Rodríguez-Revenga L, Álvarez-Mora MI, Arteche-López A, Díaz de Bustamante A, Calvo R, Pujol A, Azkargorta M, Elortza F, Malagelada C, Pinyol R, Huguet-Pradell J, Melgar-Lesmes P, Jiménez W, Morales-Ruiz M. Tcf20 deficiency is associated with increased liver fibrogenesis and alterations in mitochondrial metabolism in mice and humans. Liver Int 2023; 43:1822-1836. [PMID: 37312667 DOI: 10.1111/liv.15640] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/23/2023] [Accepted: 05/28/2023] [Indexed: 06/15/2023]
Abstract
BACKGROUND & AIMS Transcription co-activator factor 20 (TCF20) is a regulator of transcription factors involved in extracellular matrix remodelling. In addition, TCF20 genomic variants in humans have been associated with impaired intellectual disability. Therefore, we hypothesized that TCF20 has several functions beyond those described in neurogenesis, including the regulation of fibrogenesis. METHODS Tcf20 knock-out (Tcf20-/- ) and Tcf20 heterozygous mice were generated by homologous recombination. TCF20 gene genotyping and expression was assessed in patients with pathogenic variants in the TCF20 gene. Neural development was investigated by immufluorescense. Mitochondrial metabolic activity was evaluated with the Seahorse analyser. The proteome analysis was carried out by gas chromatography mass-spectrometry. RESULTS Characterization of Tcf20-/- newborn mice showed impaired neural development and death after birth. In contrast, heterozygous mice were viable but showed higher CCl4 -induced liver fibrosis and a differential expression of genes involved in extracellular matrix homeostasis compared to wild-type mice, along with abnormal behavioural patterns compatible with autism-like phenotypes. Tcf20-/- embryonic livers and mouse embryonic fibroblast (MEF) cells revealed differential expression of structural proteins involved in the mitochondrial oxidative phosphorylation chain, increased rates of mitochondrial metabolic activity and alterations in metabolites of the citric acid cycle. These results parallel to those found in patients with TCF20 pathogenic variants, including alterations of the fibrosis scores (ELF and APRI) and the elevation of succinate concentration in plasma. CONCLUSIONS We demonstrated a new role of Tcf20 in fibrogenesis and mitochondria metabolism in mice and showed the association of TCF20 deficiency with fibrosis and metabolic biomarkers in humans.
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Affiliation(s)
- Bernat Córdoba-Jover
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Jordi Ribera
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Irene Portolés
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Elena Lecue
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Juan Rodriguez-Vita
- Tumour-Stroma Communication Laboratory, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Leticia Pérez-Sisqués
- Department of Biomedicine-Biochemistry Unit, School of Medicine University of Barcelona, Barcelona, Spain
| | - Francesco Mannara
- Institut d'Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Barcelona, Spain
| | - Estel Solsona-Vilarrasa
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Cell Death and Proliferation, Institute of Biomedical Research of Barcelona (IIBB), Consejo Superior Investigaciones Científicas (CSIC), Liver Unit, Hospital Clínic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - Carmen García-Ruiz
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Cell Death and Proliferation, Institute of Biomedical Research of Barcelona (IIBB), Consejo Superior Investigaciones Científicas (CSIC), Liver Unit, Hospital Clínic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
- USC Research Center for ALPD, Keck School of Medicine, Los Angeles, California, USA
| | - José C Fernández-Checa
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Cell Death and Proliferation, Institute of Biomedical Research of Barcelona (IIBB), Consejo Superior Investigaciones Científicas (CSIC), Liver Unit, Hospital Clínic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
- USC Research Center for ALPD, Keck School of Medicine, Los Angeles, California, USA
| | - Gregori Casals
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Department of Biomedicine-Biochemistry Unit, School of Medicine University of Barcelona, Barcelona, Spain
| | - Laia Rodríguez-Revenga
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- CIBER of Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - María Isabel Álvarez-Mora
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- CIBER of Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Genetics Department, 12 de Octubre University Hospital, Madrid, Spain
| | - Ana Arteche-López
- Genetics Department, 12 de Octubre University Hospital, Madrid, Spain
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain
| | | | - Rosa Calvo
- Institut d'Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Barcelona, Spain
- Department of Child and Adolescent Psychiatry and Psychology, Hospital Clinic of Barcelona. School of Medicine, University of Barcelona, Centro de Investigación Biomédica en Red Salud Mental (CIBERSAM), Madrid, Spain
| | - Anna Pujol
- Unidad de Animales Transgénicos UAT-CBATEG, Universitat Autònoma de Barcelona, Cerdanyola del Valles, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, Derio, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, Derio, Spain
| | - Cristina Malagelada
- Department of Biomedicine-Biochemistry Unit, School of Medicine University of Barcelona, Barcelona, Spain
| | - Roser Pinyol
- Translational Research in Hepatic Oncology Group, Liver Unit, IDIBAPS, Barcelona Clínic Hospital, University of Barcelona, Barcelona, Spain
| | - Júlia Huguet-Pradell
- Translational Research in Hepatic Oncology Group, Liver Unit, IDIBAPS, Barcelona Clínic Hospital, University of Barcelona, Barcelona, Spain
| | - Pedro Melgar-Lesmes
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Department of Biomedicine-Biochemistry Unit, School of Medicine University of Barcelona, Barcelona, Spain
| | - Wladimiro Jiménez
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Department of Biomedicine-Biochemistry Unit, School of Medicine University of Barcelona, Barcelona, Spain
| | - Manuel Morales-Ruiz
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Department of Biomedicine-Biochemistry Unit, School of Medicine University of Barcelona, Barcelona, Spain
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8
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Gil M, Azkargorta M, Fuster C, Martínez-Gómez M, Raurell I, Barberá A, Pericàs JM, Hide D, Elortza F, Genescà J, Martell M. Proteomic Analysis of Dysfunctional Liver Sinusoidal Endothelial Cells Reveals Substantial Differences in Most Common Experimental Models of Chronic Liver Diseases. Int J Mol Sci 2023; 24:11904. [PMID: 37569282 PMCID: PMC10418749 DOI: 10.3390/ijms241511904] [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: 06/07/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/13/2023] Open
Abstract
Molecular markers of dedifferentiation of dysfunctional liver sinusoidal endothelial cells (LSEC) have not been fully elucidated. We aimed at deciphering the molecular profile of dysfunctional LSEC in different pathological scenarios. Flow cytometry was used to sort CD11b-/CD32b+ and CD11b-/CD32b- LSEC from three rat models of liver disease (bile duct ligation-BDL; inhaled carbon tetrachloride-CCl4; and high fat glucose/fructose diet-HFGFD). A full proteomic profile was performed applying nano-scale liquid chromatography tandem mass spectrometry (nLC-MS) and analyzed with PEAKS software. The percentage of CD32b- LSEC varied across groups, suggesting different capillarization processes. Both CD32+ and CD32b- LSEC from models are different from control LSEC, but differently expressed proteins in CD32b- LSEC are significantly higher. Heatmaps evidenced specific protein expression patterns for each model. Analysis of biological significance comparing dysfunctional CD32b- LSEC with specialized CD32b+ LSEC from controls showed central similarities represented by 45 common down-regulated proteins involved in the suppression of the endocytic machinery and 63 common up-regulated proteins associated with the actin-dependent cytoskeleton reorganization. In summary; substantial differences but also similarities in dysfunctional LSEC from the three most common models of liver disease were found, supporting the idea that LSEC may harbor different protein expression profiles according to the etiology or disease stage.
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Affiliation(s)
- Mar Gil
- Liver Diseases, Vall d’Hebron Institut de Recerca (VHIR), Liver Unit, Hospital Universitari Vall d’Hebron (HUVH), Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (M.G.); (C.F.); (M.M.-G.); (I.R.); (A.B.); (J.M.P.); (D.H.)
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, BRTA (Basque Research & Technology Alliance), Bizkaia Science and Technology Park, 48160 Derio, Spain; (M.A.); (F.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Carla Fuster
- Liver Diseases, Vall d’Hebron Institut de Recerca (VHIR), Liver Unit, Hospital Universitari Vall d’Hebron (HUVH), Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (M.G.); (C.F.); (M.M.-G.); (I.R.); (A.B.); (J.M.P.); (D.H.)
| | - María Martínez-Gómez
- Liver Diseases, Vall d’Hebron Institut de Recerca (VHIR), Liver Unit, Hospital Universitari Vall d’Hebron (HUVH), Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (M.G.); (C.F.); (M.M.-G.); (I.R.); (A.B.); (J.M.P.); (D.H.)
| | - Imma Raurell
- Liver Diseases, Vall d’Hebron Institut de Recerca (VHIR), Liver Unit, Hospital Universitari Vall d’Hebron (HUVH), Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (M.G.); (C.F.); (M.M.-G.); (I.R.); (A.B.); (J.M.P.); (D.H.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Aurora Barberá
- Liver Diseases, Vall d’Hebron Institut de Recerca (VHIR), Liver Unit, Hospital Universitari Vall d’Hebron (HUVH), Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (M.G.); (C.F.); (M.M.-G.); (I.R.); (A.B.); (J.M.P.); (D.H.)
| | - Juan Manuel Pericàs
- Liver Diseases, Vall d’Hebron Institut de Recerca (VHIR), Liver Unit, Hospital Universitari Vall d’Hebron (HUVH), Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (M.G.); (C.F.); (M.M.-G.); (I.R.); (A.B.); (J.M.P.); (D.H.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Diana Hide
- Liver Diseases, Vall d’Hebron Institut de Recerca (VHIR), Liver Unit, Hospital Universitari Vall d’Hebron (HUVH), Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (M.G.); (C.F.); (M.M.-G.); (I.R.); (A.B.); (J.M.P.); (D.H.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, BRTA (Basque Research & Technology Alliance), Bizkaia Science and Technology Park, 48160 Derio, Spain; (M.A.); (F.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Joan Genescà
- Liver Diseases, Vall d’Hebron Institut de Recerca (VHIR), Liver Unit, Hospital Universitari Vall d’Hebron (HUVH), Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (M.G.); (C.F.); (M.M.-G.); (I.R.); (A.B.); (J.M.P.); (D.H.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - María Martell
- Liver Diseases, Vall d’Hebron Institut de Recerca (VHIR), Liver Unit, Hospital Universitari Vall d’Hebron (HUVH), Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (M.G.); (C.F.); (M.M.-G.); (I.R.); (A.B.); (J.M.P.); (D.H.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
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9
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Lapitz A, Azkargorta M, Milkiewicz P, Olaizola P, Zhuravleva E, Grimsrud MM, Schramm C, Arbelaiz A, O'Rourke CJ, La Casta A, Milkiewicz M, Pastor T, Vesterhus M, Jimenez-Agüero R, Dill MT, Lamarca A, Valle JW, Macias RIR, Izquierdo-Sanchez L, Pérez Castaño Y, Caballero-Camino FJ, Riaño I, Krawczyk M, Ibarra C, Bustamante J, Nova-Camacho LM, Falcon-Perez JM, Elortza F, Perugorria MJ, Andersen JB, Bujanda L, Karlsen TH, Folseraas T, Rodrigues PM, Banales JM. Liquid biopsy-based protein biomarkers for risk prediction, early diagnosis, and prognostication of cholangiocarcinoma. J Hepatol 2023; 79:93-108. [PMID: 36868481 PMCID: PMC10292605 DOI: 10.1016/j.jhep.2023.02.027] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [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: 11/19/2021] [Revised: 02/09/2023] [Accepted: 02/15/2023] [Indexed: 03/05/2023]
Abstract
BACKGROUND & AIMS Cholangiocarcinoma (CCA), heterogeneous biliary tumours with dismal prognosis, lacks accurate early diagnostic methods especially important for individuals at high-risk (i.e. those with primary sclerosing cholangitis [PSC]). Here, we searched for protein biomarkers in serum extracellular vesicles (EVs). METHODS EVs from patients with isolated PSC (n = 45), concomitant PSC-CCA (n = 44), PSC who developed CCA during follow-up (PSC to CCA; n = 25), CCAs from non-PSC aetiology (n = 56), and hepatocellular carcinoma (n = 34) and healthy individuals (n = 56) were characterised by mass spectrometry. Diagnostic biomarkers for PSC-CCA, non-PSC CCA, or CCAs regardless of aetiology (Pan-CCAs) were defined and validated by ELISA. Their expression was evaluated in CCA tumours at a single-cell level. Prognostic EV biomarkers for CCA were investigated. RESULTS High-throughput proteomics of EVs identified diagnostic biomarkers for PSC-CCA, non-PSC CCA, or Pan-CCA, and for the differential diagnosis of intrahepatic CCA and hepatocellular carcinoma, which were cross-validated by ELISA using total serum. Machine learning-based algorithms disclosed CRP/FIBRINOGEN/FRIL for the diagnosis of PSC-CCA (local disease [LD]) vs. isolated PSC (AUC = 0.947; odds ratio [OR] =36.9) and, combined with carbohydrate antigen 19-9, overpowers carbohydrate antigen 19-9 alone. CRP/PIGR/VWF allowed the diagnosis of LD non-PSC CCAs vs. healthy individuals (AUC = 0.992; OR = 387.5). It is noteworthy that CRP/FRIL accurately diagnosed LD Pan-CCA (AUC = 0.941; OR = 89.4). Levels of CRP/FIBRINOGEN/FRIL/PIGR showed predictive capacity for CCA development in PSC before clinical evidence of malignancy. Multi-organ transcriptomic analysis revealed that serum EV biomarkers were mostly expressed in hepatobiliary tissues, and single-cell RNA sequencing and immunofluorescence analysis of CCA tumours showed their presence mainly in malignant cholangiocytes. Multivariable analysis unveiled EV prognostic biomarkers, with COMP/GNAI2/CFAI and ACTN1/MYCT1/PF4V associated negatively and positively with patients' survival, respectively. CONCLUSIONS Serum EVs contain protein biomarkers for the prediction, early diagnosis, and prognostication of CCA that are detectable using total serum, representing a tumour cell-derived liquid biopsy tool for personalised medicine. IMPACT AND IMPLICATIONS The accuracy of current imaging tests and circulating tumour biomarkers for cholangiocarcinoma (CCA) diagnosis is far from satisfactory. Most CCAs are considered sporadic, although up to 20% of patients with primary sclerosing cholangitis (PSC) develop CCA during their lifetime, constituting a major cause of PSC-related death. This international study has proposed protein-based and aetiology-related logistic models with predictive, diagnostic, or prognostic capacities by combining two to four circulating protein biomarkers, moving a step forward into personalised medicine. These novel liquid biopsy tools may allow the (i) easy and non-invasive diagnosis of sporadic CCAs, (ii) identification of patients with PSC with higher risk for CCA development, (iii) establishment of cost-effective surveillance programmes for the early detection of CCA in high-risk populations (e.g. PSC), and (iv) prognostic stratification of patients with CCA, which, altogether, may increase the number of cases eligible for potentially curative options or to receive more successful treatments, decreasing CCA-related mortality.
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Affiliation(s)
- Ainhoa Lapitz
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC BioGUNE, Basque Research and Technology Alliance (BRTA), ProteoRed ISCIII, Bizkaia Science and Technology Park, Derio, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd), ISCIII, Madrid, Spain
| | - Piotr Milkiewicz
- Liver and Internal Medicine Unit, Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland; Translational Medicine Group, Pomeranian Medical University, Szczecin, Poland
| | - Paula Olaizola
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health 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), ISCIII, Madrid, Spain
| | - Ekaterina Zhuravleva
- Biotech Research and Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marit M Grimsrud
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Christoph Schramm
- European Reference Network Hepatological Diseases (ERN RARE-LIVER), Hamburg, Germany; 1st Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Martin Zeitz Centre for Rare Diseases, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - 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
| | - Colm J O'Rourke
- Biotech Research and Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Adelaida La Casta
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Malgorzata Milkiewicz
- Department of Medical Biology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Tania Pastor
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Mette Vesterhus
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway; Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Raul Jimenez-Agüero
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Michael T Dill
- Department of Gastroenterology, Infectious Diseases and Intoxication, Heidelberg University Hospital, Heidelberg, Germany; Experimental Hepatology, Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angela Lamarca
- Department of Medical Oncology, The Christie NHS Foundation Trust/Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Juan W Valle
- Department of Medical Oncology, The Christie NHS Foundation Trust/Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Rocio I R Macias
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd), ISCIII, Madrid, Spain; Experimental Hepatology and Drug Targeting (HEVEPHARM), University of Salamanca, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain
| | - Laura Izquierdo-Sanchez
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health 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), ISCIII, Madrid, Spain
| | - Ylenia Pérez Castaño
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain; Osakidetza Basque Health Service, Bidasoa IHO, Bidasoa Hospital, Department of Digestive System, Irun, Spain
| | - Francisco Javier Caballero-Camino
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Ioana Riaño
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain; Clinical Research Unit, Spanish Clinical Research Network (SCReN) - ISCIII, Biodonostia Health Research Institute, San Sebastián, Spain
| | - Marcin Krawczyk
- Department of Medicine II, Saarland University Medical Centre, Saarland University, Homburg, Germany
| | - Cesar Ibarra
- Osakidetza Basque Health Service, Ezkerraldea-Enkarterri-Cruces IHO, Cruces University Hospital, Barakaldo, Spain
| | - Javier Bustamante
- Osakidetza Basque Health Service, Ezkerraldea-Enkarterri-Cruces IHO, Cruces University Hospital, Barakaldo, Spain
| | - Luiz M Nova-Camacho
- Osakidetza Basque Health Service, Donostialdea IHO, Donostia University Hospital, Department of Pathology, San Sebastian, Spain
| | - Juan M Falcon-Perez
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd), ISCIII, Madrid, Spain; Center for Cooperative Research in Biosciences (CIC BioGUNE), Basque Research and Technology Alliance (BRTA), Exosomes Laboratory, Derio, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Felix Elortza
- Proteomics Platform, CIC BioGUNE, Basque Research and Technology Alliance (BRTA), ProteoRed ISCIII, Bizkaia Science and Technology Park, Derio, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd), ISCIII, Madrid, Spain
| | - Maria J Perugorria
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health 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), ISCIII, Madrid, Spain; Department of Medicine, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Jesper B Andersen
- Biotech Research and Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Luis Bujanda
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health 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), ISCIII, Madrid, Spain; Department of Medicine, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Tom H Karlsen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Trine Folseraas
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway; Section of Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Pedro M Rodrigues
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health 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), ISCIII, Madrid, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
| | - Jesus M Banales
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health 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), ISCIII, Madrid, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain; Department of Biochemistry and Genetics, School of Sciences, University of Navarra, Pamplona, Spain.
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10
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Lenza MP, Egia-Mendikute L, Antoñana-Vildosola A, Soares CO, Coelho H, Corzana F, Bosch A, Manisha P, Quintana JI, Oyenarte I, Unione L, Moure MJ, Azkargorta M, Atxabal U, Sobczak K, Elortza F, Sutherland JD, Barrio R, Marcelo F, Jiménez-Barbero J, Palazon A, Ereño-Orbea J. Structural insights into Siglec-15 reveal glycosylation dependency for its interaction with T cells through integrin CD11b. Nat Commun 2023; 14:3496. [PMID: 37311743 DOI: 10.1038/s41467-023-39119-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 05/26/2023] [Indexed: 06/15/2023] Open
Abstract
Sialic acid-binding Ig-like lectin 15 (Siglec-15) is an immune modulator and emerging cancer immunotherapy target. However, limited understanding of its structure and mechanism of action restrains the development of drug candidates that unleash its full therapeutic potential. In this study, we elucidate the crystal structure of Siglec-15 and its binding epitope via co-crystallization with an anti-Siglec-15 blocking antibody. Using saturation transfer-difference nuclear magnetic resonance (STD-NMR) spectroscopy and molecular dynamics simulations, we reveal Siglec-15 binding mode to α(2,3)- and α(2,6)-linked sialic acids and the cancer-associated sialyl-Tn (STn) glycoform. We demonstrate that binding of Siglec-15 to T cells, which lack STn expression, depends on the presence of α(2,3)- and α(2,6)-linked sialoglycans. Furthermore, we identify the leukocyte integrin CD11b as a Siglec-15 binding partner on human T cells. Collectively, our findings provide an integrated understanding of the structural features of Siglec-15 and emphasize glycosylation as a crucial factor in controlling T cell responses.
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Affiliation(s)
- Maria Pia Lenza
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 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), Bizkaia Technology Park, Building 801A, 48160, 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), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Cátia O Soares
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Caparica campus, 2829-516, Caparica, Portugal
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Caparica campus, 2829-516, Caparica, Portugal
| | - Helena Coelho
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Caparica campus, 2829-516, Caparica, Portugal
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Caparica campus, 2829-516, Caparica, Portugal
| | - Francisco Corzana
- Department of Chemistry, University of La Rioja, The Center for Research in Chemical Synthesis, Madre de Dios 53, E-26006, Logroño, Spain
| | - Alexandre Bosch
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Prodhi Manisha
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Jon Imanol Quintana
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Iker Oyenarte
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Luca Unione
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - María Jesús Moure
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Spain
| | - Unai Atxabal
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Klaudia Sobczak
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Spain
| | - James D Sutherland
- Ubiquitin-likes and Development Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 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), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Filipa Marcelo
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Caparica campus, 2829-516, Caparica, Portugal
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Caparica campus, 2829-516, Caparica, Portugal
| | - Jesús Jiménez-Barbero
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
- Department of Organic & Inorganic Chemistry, Faculty of Science and Technology, University of the Basque Country, EHU-UPV, 48940, Leioa, Bizkaia, Spain.
- Centro de Investigacion Biomedica En Red de Enfermedades Respiratorias, 28029, Madrid, Spain.
| | - Asis Palazon
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
| | - June Ereño-Orbea
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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11
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Goñi N, Martínez‐Soroa I, Ibarrondo O, Azkargorta M, Elortza F, Galarreta D, Bidaguren A, Juaristi L, Acera A. Tear proteome profile in eyes with keratoconus after intracorneal ring segment implantation or corneal crosslinking. Acta Ophthalmol 2022. [DOI: 10.1111/j.1755-3768.2022.0520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Nahia Goñi
- Ophthalmology Hospital de Zumárraga Zumárraga Spain
- Ophthalmology University of the Basque Country UPV/EHU Leioa Spain
| | - Itziar Martínez‐Soroa
- Ophthalmology University of the Basque Country UPV/EHU Leioa Spain
- Ophthalmology Hospital Universitario Donostia San Sebastian Spain
| | | | - Mikel Azkargorta
- Center for Cooperative Research in Biosciences, Department of Proteomics Derio Spain
| | - Felix Elortza
- Center for Cooperative Research in Biosciences, Department of Proteomics Derio Spain
| | - David Galarreta
- Hospital Clinico Universitario de Valladolid, Ophthalmology Valladolid Spain
| | - Aritz Bidaguren
- Ophthalmology University of the Basque Country UPV/EHU Leioa Spain
- Ophthalmology Hospital Universitario Donostia San Sebastian Spain
| | - Leire Juaristi
- Ophthalmology Hospital Universitario Donostia San Sebastian Spain
| | - Arantxa Acera
- Department of Cell Biology and Histology, Experimental Ophthalmo‐Biology Group University of the Basque Country UPV/EHU Leioa Spain
- IKERBASQUE, Basque Foundation for Science Bilbao Spain
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12
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Ruiz de Gauna M, Biancaniello F, González-Romero F, Rodrigues PM, Lapitz A, Gómez-Santos B, Olaizola P, Di Matteo S, Aurrekoetxea I, Labiano I, Nieva-Zuluaga A, Benito-Vicente A, Perugorria MJ, Apodaka-Biguri M, Paiva NA, Sáenz de Urturi D, Buqué X, Delgado I, Martín C, Azkargorta M, Elortza F, Calvisi DF, Andersen JB, Alvaro D, Cardinale V, Bujanda L, Banales JM, Aspichueta P. Cholangiocarcinoma progression depends on the uptake and metabolization of extracellular lipids. Hepatology 2022; 76:1617-1633. [PMID: 35030285 PMCID: PMC9790564 DOI: 10.1002/hep.32344] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 12/17/2021] [Accepted: 12/17/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND AND AIMS Cholangiocarcinoma (CCA) includes a heterogeneous group of biliary cancers with a dismal prognosis. We investigated if lipid metabolism is disrupted in CCA and its role in tumor proliferation. APPROACH AND RESULTS The in vitro and in vivo tumorigenic capacity of five human CCA cell lines was analyzed. Proteome, lipid content, and metabolic fluxes were evaluated in CCA cells and compared with normal human cholangiocytes (NHC). The Akt1/NOTCH1 intracellular cytoplasmic domain (Nicd1)-driven CCA mouse model was also evaluated. The proteome of CCA cells was enriched in pathways involved in lipid and lipoprotein metabolism. The EGI1 CCA cell line presented the highest tumorigenic capacity. Metabolic studies in high (EGI1) versus low (HUCCT1) proliferative CCA cells in vitro showed that both EGI1 and HUCCT1 incorporated more fatty acids (FA) than NHC, leading to increased triglyceride storage, also observed in Akt1/Nicd1-driven CCA mouse model. The highly proliferative EGI1 CCA cells showed greater uptake of very-low-density and HDLs than NHC and HUCCT1 CCA cells and increased cholesteryl ester content. The FA oxidation (FAO) and related proteome enrichment were specifically up-regulated in EGI1, and consequently, pharmacological blockade of FAO induced more pronounced inhibition of their tumorigenic capacity compared with HUCCT1. The expression of acyl-CoA dehydrogenase ACADM, the first enzyme involved in FAO, was increased in human CCA tissues and correlated with the proliferation marker PCNA. CONCLUSIONS Highly proliferative human CCA cells rely on lipid and lipoprotein uptake to fuel FA catabolism, suggesting that inhibition of FAO and/or lipid uptake could represent a therapeutic strategy for this CCA subclass.
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Affiliation(s)
- Mikel Ruiz de Gauna
- Faculty of Medicine and NursingDepartment of PhysiologyUniversity of the Basque Country (UPV/EHU)LeioaSpain
| | - Francesca Biancaniello
- Department of Liver and Gastrointestinal DiseasesBiodonostia Health Research InstituteDonostia University HospitalUniversity of the Basque Country (UPV/EHU)San SebastianSpain.,Department of Translational and Precision Medicine"Sapienza" University of RomeRomeItaly
| | - Francisco González-Romero
- Faculty of Medicine and NursingDepartment of PhysiologyUniversity of the Basque Country (UPV/EHU)LeioaSpain
| | - Pedro M Rodrigues
- Department of Liver and Gastrointestinal DiseasesBiodonostia Health Research InstituteDonostia University HospitalUniversity of the Basque Country (UPV/EHU)San SebastianSpain.,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehdCarlos III Health Institute)MadridSpain.,IKERBASQUEBasque Foundation for ScienceBilbaoSpain
| | - Ainhoa Lapitz
- Department of Liver and Gastrointestinal DiseasesBiodonostia Health Research InstituteDonostia University HospitalUniversity of the Basque Country (UPV/EHU)San SebastianSpain
| | - Beatriz Gómez-Santos
- Faculty of Medicine and NursingDepartment of PhysiologyUniversity of the Basque Country (UPV/EHU)LeioaSpain
| | - Paula Olaizola
- Department of Liver and Gastrointestinal DiseasesBiodonostia Health Research InstituteDonostia University HospitalUniversity of the Basque Country (UPV/EHU)San SebastianSpain
| | - Sabina Di Matteo
- Department of Liver and Gastrointestinal DiseasesBiodonostia Health Research InstituteDonostia University HospitalUniversity of the Basque Country (UPV/EHU)San SebastianSpain.,Department of Translational and Precision Medicine"Sapienza" University of RomeRomeItaly
| | - Igor Aurrekoetxea
- Faculty of Medicine and NursingDepartment of PhysiologyUniversity of the Basque Country (UPV/EHU)LeioaSpain.,Biocruces Bizkaia Health Research InstituteCruces University HospitalBarakaldoSpain
| | - Ibone Labiano
- Department of Liver and Gastrointestinal DiseasesBiodonostia Health Research InstituteDonostia University HospitalUniversity of the Basque Country (UPV/EHU)San SebastianSpain
| | - Ane Nieva-Zuluaga
- Faculty of Medicine and NursingDepartment of PhysiologyUniversity of the Basque Country (UPV/EHU)LeioaSpain
| | - Asier Benito-Vicente
- Department of Molecular BiophysicsBiofisika Institute (University of Basque Country and Consejo Superior de Investigaciones Científicas (UPV/EHU, CSIC)LeioaSpain.,Department of Biochemistry and Molecular BiologyUniversity of the Basque Country (UPV/EHU)LeioaSpain
| | - María J Perugorria
- Department of Liver and Gastrointestinal DiseasesBiodonostia Health Research InstituteDonostia University HospitalUniversity of the Basque Country (UPV/EHU)San SebastianSpain.,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehdCarlos III Health Institute)MadridSpain
| | - Maider Apodaka-Biguri
- Faculty of Medicine and NursingDepartment of PhysiologyUniversity of the Basque Country (UPV/EHU)LeioaSpain
| | - Nuno A Paiva
- Department of Liver and Gastrointestinal DiseasesBiodonostia Health Research InstituteDonostia University HospitalUniversity of the Basque Country (UPV/EHU)San SebastianSpain
| | - Diego Sáenz de Urturi
- Faculty of Medicine and NursingDepartment of PhysiologyUniversity of the Basque Country (UPV/EHU)LeioaSpain
| | - Xabier Buqué
- Faculty of Medicine and NursingDepartment of PhysiologyUniversity of the Basque Country (UPV/EHU)LeioaSpain
| | - Igotz Delgado
- Faculty of Medicine and NursingDepartment of PhysiologyUniversity of the Basque Country (UPV/EHU)LeioaSpain
| | - César Martín
- Department of Molecular BiophysicsBiofisika Institute (University of Basque Country and Consejo Superior de Investigaciones Científicas (UPV/EHU, CSIC)LeioaSpain.,Department of Biochemistry and Molecular BiologyUniversity of the Basque Country (UPV/EHU)LeioaSpain
| | - Mikel Azkargorta
- Proteomics PlatformCIC bioGUNEBRTA (Basque Research and Technology Alliance)ProteoRed-ISCIIICIBERehdBizkaia Science and Technology ParkDerioSpain
| | - Felix Elortza
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehdCarlos III Health Institute)MadridSpain.,Proteomics PlatformCIC bioGUNEBRTA (Basque Research and Technology Alliance)ProteoRed-ISCIIICIBERehdBizkaia Science and Technology ParkDerioSpain
| | - Diego F Calvisi
- Institute of PathologyUniversity of RegensburgRegensburgGermany
| | - Jesper B Andersen
- Biotech Research & Innovation Centre (BRIC)Department of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Domenico Alvaro
- Department of Translational and Precision Medicine"Sapienza" University of RomeRomeItaly
| | - Vincenzo Cardinale
- Department of Medico-Surgical Sciences and Biotechnology"Sapienza" University of RomeRomeItaly
| | - Luis Bujanda
- Department of Liver and Gastrointestinal DiseasesBiodonostia Health Research InstituteDonostia University HospitalUniversity of the Basque Country (UPV/EHU)San SebastianSpain.,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehdCarlos III Health Institute)MadridSpain
| | - Jesús M Banales
- Department of Liver and Gastrointestinal DiseasesBiodonostia Health Research InstituteDonostia University HospitalUniversity of the Basque Country (UPV/EHU)San SebastianSpain.,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehdCarlos III Health Institute)MadridSpain.,IKERBASQUEBasque Foundation for ScienceBilbaoSpain.,Department of Biochemistry and GeneticsSchool of SciencesUniversity of NavarraPamplonaSpain
| | - Patricia Aspichueta
- Faculty of Medicine and NursingDepartment of PhysiologyUniversity of the Basque Country (UPV/EHU)LeioaSpain.,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehdCarlos III Health Institute)MadridSpain.,Biocruces Bizkaia Health Research InstituteCruces University HospitalBarakaldoSpain
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13
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García-Arnáez I, Romero-Gavilán F, Cerqueira A, Elortza F, Azkargorta M, Muñoz F, Mata M, de Llano JM, Suay J, Gurruchaga M, Goñi I. Correlation between biological responses in vitro and in vivo to Ca-doped sol-gel coatings assessed using proteomic analysis. Colloids Surf B Biointerfaces 2022; 220:112962. [DOI: 10.1016/j.colsurfb.2022.112962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/10/2022] [Accepted: 10/20/2022] [Indexed: 11/13/2022]
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14
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Goñi N, Martínez-Soroa I, Ibarrondo O, Azkargorta M, Elortza F, Galarreta DJ, Acera A. Tear proteome profile in eyes with keratoconus after intracorneal ring segment implantation or corneal crosslinking. Front Med (Lausanne) 2022; 9:944504. [PMID: 36203781 PMCID: PMC9531826 DOI: 10.3389/fmed.2022.944504] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
PurposeKeratoconus (KC) is a corneal ectasia characterized by structural changes, resulting in progressive thinning and biomechanical weakening that can lead to worsening visual acuity due to irregular astigmatism. Corneal collagen Crosslinking (CXL) and Intracorneal Ring Segment (ICRS) are widely used treatments in KC disease, but the alterations they cause in biomechanical mediators are still poorly understood. The aim of this study was to analyze the tear proteome profile before and after treatments to identify biomarkers altered by surgery.Materials and methodsAn observational, prospective, case-control pilot study was conducted, analyzing tear samples from KC patients by nano-liquid chromatography-mass spectrometry (nLC-MS/MS). Data are available via ProteomeXchange with identifier PXD035655. Patients with KC who underwent ICRS surgery (n = 4), CXL (n = 4), and healthy subjects (Ctrl, n = 4) were included in this study. Clinical parameters were measured and tear samples were collected before and 18 months after surgery. Proteins with ≥2 expression change and p-value < 0.05 between groups and times were selected to study their role in post-operative corneal changes.ResultsThese analyses led to the identification of 447 tear proteins, some of which were dysregulated in KC patients. In comparisons between the two surgical groups and Ctrls, the biological processes that were altered in KC patients at baseline were those that were dysregulated as a consequence of the disease and not of the surgical intervention. Among the biological processes seen to be altered were: immune responses, cytoskeleton components, protein synthesis and metabolic reactions. When comparing the two treatment groups (ICRS and CXL), the process related to cytoskeleton components was the most altered, probably due to corneal thinning which was more pronounced in patients undergoing CXL.ConclusionThe changes observed in tears after 18 months post-operatively could be due to the treatments performed and the pathology. Among the deregulated proteins detected, A-kinase anchor protein 13 (AKAP-13) deserves special attention for its involvement in corneal thinning, and for its strong overexpression in the tears of patients with more active KC and faster disease progression. However, it should be kept in mind that this is a pilot study conducted in a small number of patients.
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Affiliation(s)
- Nahia Goñi
- Department of Ophthalmology, Hospital Universitario Donostia, San Sebastian, Spain
- Department of Ophthalmology, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Itziar Martínez-Soroa
- Department of Ophthalmology, Hospital Universitario Donostia, San Sebastian, Spain
- Department of Ophthalmology, University of the Basque Country UPV/EHU, Leioa, Spain
| | | | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, Derio, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, Derio, Spain
| | - David J. Galarreta
- Department of Ophthalmology, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | - Arantxa Acera
- Department of Cell Biology and Histology, Experimental Ophthalmo-Biology Group (GOBE:www.ehu.eus/gobe), University of the Basque Country UPV/EHU, Leioa, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- *Correspondence: Arantxa Acera,
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15
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Anitua E, Pino A, Azkargorta M, Elortza F, Merayo-Lloves J, Muruzabal F. Differential Protein Content between Fresh and Freeze-Dried Plasma Rich in Growth Factors Eye Drops. Biomolecules 2022; 12:biom12091215. [PMID: 36139054 PMCID: PMC9496081 DOI: 10.3390/biom12091215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/25/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
The purpose of this study was to analyze the proteomic composition of plasma rich in growth factors eye drops (PRGF) in comparison to lyophilized PRGF eye drops (PRGF lyo). The differential protein expression of keratocyte (HK) cells after PRGF or PRGF lyo treatment was also determined. Blood from different donors was collected and processed to obtain PRGF and PRGF lyo eye drops. Then, HK cells were treated with both formulations. A proteomic analysis was performed to evaluate the differential proteomic profile between PRGF and PRGF lyo, and the differential protein expression by HK cells after treatment with both blood-derived products. About 280 proteins were detected between both blood-derived formulation, with only 8 of them reaching significant differences. Furthermore, 101 out of 3213 proteins showed statistically significant deregulation in HK cells after treatment with PRGF or PRGF lyo. Gene Ontology analysis showed that these significant deregulated proteins were involved in 30 functional processes. However, the Ingenuity Pathway Analysis showed that no significant differences were found in any of the identified processes. In summary, the present study show that no significant differences were found in the proteomic profile or in the signaling pathways activation in HK cells between PRGF and PRGF lyo.
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Affiliation(s)
- Eduardo Anitua
- BTI—Biotechnology Institute, 01007 Vitoria, Spain
- Research and Development Department, University Institute for Regenerative Medicine and Oral Implantology—UIRMI (UPV/EHU-Fundación Eduardo Anitua), 01007 Vitoria, Spain
- Correspondence:
| | - Ander Pino
- BTI—Biotechnology Institute, 01007 Vitoria, Spain
- Research and Development Department, University Institute for Regenerative Medicine and Oral Implantology—UIRMI (UPV/EHU-Fundación Eduardo Anitua), 01007 Vitoria, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Jesús Merayo-Lloves
- Fundación de Investigación Oftalmológica, Instituto Oftalmológico Fernández-Vega, 33012 Oviedo, Spain
| | - Francisco Muruzabal
- BTI—Biotechnology Institute, 01007 Vitoria, Spain
- Research and Development Department, University Institute for Regenerative Medicine and Oral Implantology—UIRMI (UPV/EHU-Fundación Eduardo Anitua), 01007 Vitoria, Spain
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16
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Del Río-Álvarez Á, Carrillo-Reixach J, Royo L, Domingo-Sàbat M, Azkargorta M, Kapler R, Cairo S, Vokuhl C, de Krijger R, Alaggio R, Garrido M, Guillen G, Sábado C, Guerra L, Hernandez F, Mateos ME, López-Satamaría M, Torres B, Abad MP, Viera B, Czauderna P, Buendia MA, Elortza F, Wheatley K, Morland B, Armengol C. Abstract PO011: Proteomic profiling of childhood liver cancer: identification of novel diagnostic and prognostic biomarkers. Clin Cancer Res 2022. [DOI: 10.1158/1557-3265.liverca22-po011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Childhood liver cancers hepatoblastoma (HB) and hepatocellular carcinoma (HCC) are rare diseases but with a rising incidence. HEMNOS (Hepatocellular malignant neoplasm, not otherwise specified) is a recent entity with histopathological features of HB and HCC. Current chemotherapy treatments are effective to shrink tumor before surgery, nonetheless can cause severe lifelong adverse effects and are not effective for patients with aggressive and metastatic HB or HCC (~20% die due to the disease). The HB and HCC diagnosis is key to assign therapeutic regimens in the ongoing Pediatric Hepatic International Tumor Trial (PHITT); however, differential diagnosis for some patients is challenging due to the lack of specific biomarkers. Nowadays, there is an urgent need to identify diagnostic and prognostic biomarkers to improve the clinical management of childhood liver cancer. Herein, we aimed to uncover the proteomic profiles of different types of childhood liver cancer and identify new biomarkers for improving tumor diagnosis and early detection of the most aggressive cases. For this, 99 frozen tissue samples from 71 patients (mean age: 54.5 months, 60.6% boys, 40.9% metastasis, 23.7% deaths) including 70 primary tumors (57 HB, 8 HCC and 5 HEM-NOS), 22 non-tumors and 7 metastases were analyzed by label free mass spectrometry analysis. A total of 5,417 proteins were sequenced in the different samples. Through supervised analysis, we identified a total of 1302 differential expressed proteins in tumors as compared to non-tumor livers (FC +2 and FDR <0.01). A total of 246 proteins of them (19%) were commonly differently expressed in all tumors types; having HEMNOS a mixture of HB and HCC protein profiling. A panel of potential diagnostic biomarkers including 179, 120 and 81 upregulated proteins (FC >2) was defined for HB, HCC and HEM-NOS, respectively. Hierarchical unsupervised clustering and principal component analysis showed two main cluster of tumors: one including HB and HEM-NOS and another one with a mixture of HB, HEM-NOS and HCC. Interestingly, this second cluster was associated with clinical and molecular features of aggressive tumors such as multifocality (p = 0.029), Epigenetic Epi-CB subclass (p = 0.006), high-risk Molecular Risk Stratification (p = 0.009) and poor survival (log rank test=0.012). A total of 2082 proteins were found to be differently expressed between the two prognostic clusters (FC +2 and FDR < 0.01); the GEO enrichment analysis revealed that these proteins were significantly enriched in post-transcriptional gene silencing and RNA splicing mechanisms (FDR <10−7). In addition, a 25-protein signature associated to liver cancer prognosis was defined (FC>6 and FDR < 10−14). In conclusion, we identified a list of potential diagnostic and prognostic protein biomarkers that after a validation in large patient cohort, could be used to improve the clinical management of childhood liver cancer.
Citation Format: Álvaro Del Río-Álvarez, Juan Carrillo-Reixach, Laura Royo, Montse Domingo-Sàbat, Mikel Azkargorta, Roland Kapler, Stefano Cairo, Christian Vokuhl, Ronald de Krijger, Rita Alaggio, Marta Garrido, Gabriela Guillen, Constantino Sábado, Laura Guerra, Francisco Hernandez, Maria Elena Mateos, Manuel López-Satamaría, Barbara Torres, Maria Pilar Abad, Bajčiová Viera, Piotr Czauderna, Marie Annick Buendia, Felix Elortza, Keith Wheatley, Bruce Morland, Carolina Armengol. Proteomic profiling of childhood liver cancer: identification of novel diagnostic and prognostic biomarkers [abstract]. In: Proceedings of the AACR Special Conference: Advances in the Pathogenesis and Molecular Therapies of Liver Cancer; 2022 May 5-8; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(17_Suppl):Abstract nr PO011.
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Affiliation(s)
- Álvaro Del Río-Álvarez
- 1Childhood Liver Oncology Group (c-LOG), Health Sciences Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain., Badalona, Spain,
| | - Juan Carrillo-Reixach
- 1Childhood Liver Oncology Group (c-LOG), Health Sciences Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain., Badalona, Spain,
| | - Laura Royo
- 1Childhood Liver Oncology Group (c-LOG), Health Sciences Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain., Badalona, Spain,
| | - Montse Domingo-Sàbat
- 2Childhood Liver Oncology Group (c-LOG), Health Sciences Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain, Badalona, Spain,
| | - Mikel Azkargorta
- 3Proteomics Platform, CIC bioGUNE - ProteoRed-ISCIII, Derio, Spain., Derio, Spain,
| | - Roland Kapler
- 4Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Lindwurmstr. 2a, 80337 Munich, Germany., Munich, Germany,
| | | | - Christian Vokuhl
- 6Section of Pediatric Pathology, Department of Pathology, University Hospital Bonn, Bonn, Germany., Bonn, Germany,
| | - Ronald de Krijger
- 7Princess Maxima Centre for Pediatric Oncology, Utrecht, Netherlands., Utrecht, Netherlands,
| | - Rita Alaggio
- 8Unit of Pathology, Children's Hospital Bambino Gesù IRCCS, Rome, Italy., Rome, Italy,
| | - Marta Garrido
- 9Hospital Vall d’Hebron, Pathology Department, Barcelona, Spain, Barcelona, Spain,
| | - Gabriela Guillen
- 10Hospital Vall d’Hebron, Pediatric Surgery Department, Barcelona, Spain, Barcelona, Spain,
| | - Constantino Sábado
- 11Hospital Vall d’Hebron, Pediatric Oncology Department, Barcelona, Spain, Barcelona, Spain,
| | - Laura Guerra
- 12University Hospital La Paz, Pathology Department, Madrid, Spain, Madrid, Spain,
| | - Francisco Hernandez
- 13University Hospital La Paz, Pediatric Surgery Department, Madrid, Spain, Madrid, Spain,
| | - Maria Elena Mateos
- 14Pediatric Oncology Unit, Department of Pediatrics, University Hospital Reina Sofía, Córdoba, Spain, Cordoba, Spain,
| | - Manuel López-Satamaría
- 13University Hospital La Paz, Pediatric Surgery Department, Madrid, Spain, Madrid, Spain,
| | - Barbara Torres
- 15Medical Oncology Department, Pediatric Oncology Department, University Hospital La Fe, Valencia, Spain, Valencia, Spain,
| | - Maria Pilar Abad
- 16University Hospital Germans Trias i Pujol, Pediatric Surgery Department, Badalona, España., Badalona, SA, Spain,
| | - Bajčiová Viera
- 17Department of Pediatric Oncology, Childrens University Hospital Brno, Brno, Czech., Brno, Czech Republic,
| | - Piotr Czauderna
- 18Department of Surgery and Urology for Children and Adolescents, Medical University of Gdansk, Gdansk, Poland., Gdansk, Poland,
| | - Marie Annick Buendia
- 19INSERM, UMR 1193, Paul-Brousse Hospital, Hepatobiliary Centre F-94800 Villejuif France., Villejuif, France,
| | - Felix Elortza
- 3Proteomics Platform, CIC bioGUNE - ProteoRed-ISCIII, Derio, Spain., Derio, Spain,
| | - Keith Wheatley
- 20University of Birmingham Clinical Trials Unit, Park Grange, 1 Somerset Road, Edgbaston, Birmingham, Birmingham, United Kingdom,
| | - Bruce Morland
- 21Department of Oncology, Birmingham Women's and Children's Hospital, Birmingham, UK, Birmingham, United Kingdom
| | - Carolina Armengol
- 1Childhood Liver Oncology Group (c-LOG), Health Sciences Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain., Badalona, Spain,
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17
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Iazzolino G, Mendibil U, Arnaiz B, Ruiz-de-Angulo A, Azkargorta M, Uribe KB, Khatami N, Elortza F, Olalde B, Gomez-Vallejo V, Llop J, Abarrategi A. Decellularization of xenografted tumors provides cell-specific in vitro 3D environment. Front Oncol 2022; 12:956940. [PMID: 36059712 PMCID: PMC9434107 DOI: 10.3389/fonc.2022.956940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
In vitro cell culture studies are common in the cancer research field, and reliable biomimetic 3D models are needed to ensure physiological relevance. In this manuscript, we hypothesized that decellularized xenograft tumors can serve as an optimal 3D substrate to generate a top-down approach for in vitro tumor modeling. Multiple tumor cell lines were xenografted and the formed solid tumors were recovered for their decellularization by several techniques and further characterization by histology and proteomics techniques. Selected decellularized tumor xenograft samples were seeded with the HCC1806 human triple-negative breast cancer (TNBC) basal-like subtype cell line, and cell behavior was compared among them and with other control 2D and 3D cell culture methods. A soft treatment using Freeze-EDTA-DNAse allows proper decellularization of xenografted tumor samples. Interestingly, proteomic data show that samples decellularized from TNBC basal-like subtype xenograft models had different extracellular matrix (ECM) compositions compared to the rest of the xenograft tumors tested. The in vitro recellularization of decellularized ECM (dECM) yields tumor-type–specific cell behavior in the TNBC context. Data show that dECM derived from xenograft tumors is a feasible substrate for reseeding purposes, thereby promoting tumor-type–specific cell behavior. These data serve as a proof-of-concept for further potential generation of patient-specific in vitro research models.
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Affiliation(s)
- Gaia Iazzolino
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastian, Spain
| | - Unai Mendibil
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastian, Spain
- TECNALIA, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastian, Spain
| | - Blanca Arnaiz
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastian, Spain
| | - Ane Ruiz-de-Angulo
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastian, Spain
| | - Mikel Azkargorta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Kepa B. Uribe
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastian, Spain
| | - Neda Khatami
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastian, Spain
| | - Felix Elortza
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Beatriz Olalde
- TECNALIA, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastian, Spain
| | - Vanessa Gomez-Vallejo
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastian, Spain
| | - Jordi Llop
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastian, Spain
| | - Ander Abarrategi
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastian, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- *Correspondence: Ander Abarrategi,
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18
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Mercado-Gómez M, Prieto-Fernández E, Goikoetxea-Usandizaga N, Vila-Vecilla L, Azkargorta M, Bravo M, Serrano-Maciá M, Egia-Mendikute L, Rodríguez-Agudo R, Lachiondo-Ortega S, Lee SY, Eguileor Giné A, Gil-Pitarch C, González-Recio I, Simón J, Petrov P, Jover R, Martínez-Cruz LA, Ereño-Orbea J, Delgado TC, Elortza F, Jiménez-Barbero J, Nogueiras R, Prevot V, Palazon A, Martínez-Chantar ML. The spike of SARS-CoV-2 promotes metabolic rewiring in hepatocytes. Commun Biol 2022; 5:827. [PMID: 35978143 PMCID: PMC9383691 DOI: 10.1038/s42003-022-03789-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 09/28/2021] [Accepted: 08/02/2022] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes a multi-organ damage that includes hepatic dysfunction, which has been observed in over 50% of COVID-19 patients. Liver injury in COVID-19 could be attributed to the cytopathic effects, exacerbated immune responses or treatment-associated drug toxicity. Herein we demonstrate that hepatocytes are susceptible to infection in different models: primary hepatocytes derived from humanized angiotensin-converting enzyme-2 mice (hACE2) and primary human hepatocytes. Pseudotyped viral particles expressing the full-length spike of SARS-CoV-2 and recombinant receptor binding domain (RBD) bind to ACE2 expressed by hepatocytes, promoting metabolic reprogramming towards glycolysis but also impaired mitochondrial activity. Human and hACE2 primary hepatocytes, where steatosis and inflammation were induced by methionine and choline deprivation, are more vulnerable to infection. Inhibition of the renin-angiotensin system increases the susceptibility of primary hepatocytes to infection with pseudotyped viral particles. Metformin, a common therapeutic option for hyperglycemia in type 2 diabetes patients known to partially attenuate fatty liver, reduces the infection of human and hACE2 hepatocytes. In summary, we provide evidence that hepatocytes are amenable to infection with SARS-CoV-2 pseudovirus, and we propose that metformin could be a therapeutic option to attenuate infection by SARS-CoV-2 in patients with fatty liver. SARS-CoV-2 pseudovirus infects human hepatocytes leading to metabolic reprogramming towards glycolysis and impaired mitochondrial activity, and metformin can reduce infection under steatotic conditions.
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Affiliation(s)
- Maria Mercado-Gómez
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Endika Prieto-Fernández
- Cancer Immunology and Immunotherapy Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Naroa Goikoetxea-Usandizaga
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Laura Vila-Vecilla
- Cancer Immunology and Immunotherapy Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), ProteoRedISCIII, 48160, Derio, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Miren Bravo
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Marina Serrano-Maciá
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Leire Egia-Mendikute
- Cancer Immunology and Immunotherapy Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Rubén Rodríguez-Agudo
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Sofia Lachiondo-Ortega
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - So Young Lee
- Cancer Immunology and Immunotherapy Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Alvaro Eguileor Giné
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Clàudia Gil-Pitarch
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Irene González-Recio
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Jorge Simón
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Petar Petrov
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029, Madrid, Spain.,Experimental Hepatology Joint Research Unit, IIS Hospital La Fe, Valencia, Spain
| | - Ramiro Jover
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029, Madrid, Spain.,Experimental Hepatology Joint Research Unit, IIS Hospital La Fe, Valencia, Spain.,Dep. Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| | - Luis Alfonso Martínez-Cruz
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - June Ereño-Orbea
- Chemical Glycobiology Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain.,Department of Organic Chemistry, University of the Basque Country, UPV/EHU, 48940, Leioa, Spain
| | - Teresa Cardoso Delgado
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), ProteoRedISCIII, 48160, Derio, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Jesús Jiménez-Barbero
- Chemical Glycobiology Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain.,Department of Organic Chemistry, University of the Basque Country, UPV/EHU, 48940, Leioa, Spain.,Centro de Investigación Biomédica En Red de Enfermedades Respiratorias (CIBERES), 28029, Madrid, Spain
| | - Ruben Nogueiras
- Department of Physiology, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela-Instituto de Investigación Sanitaria, CIBER Fisiopatología de a Obesidad y Nutrición (CIBERobn), Galician Agency of Innovation (GAIN), Xunta de Galicia, 15782, Santiago de Compostela, Spain
| | - Vincent Prevot
- Univ. Lille, Inserm, CHU Lille, Development and Plasticity of the Neuroendocrine Brain Lab, UMR-S1172 INSERM, DISTALZ, EGID, Lille, France
| | - Asis Palazon
- Cancer Immunology and Immunotherapy Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain. .,Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
| | - María L Martínez-Chantar
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029, Madrid, Spain.
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19
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Olaizola P, Lee-Law PY, Fernandez-Barrena MG, Alvarez L, Cadamuro M, Azkargorta M, O'Rourke CJ, Caballero-Camino FJ, Olaizola I, Macias RIR, Marin JJG, Serrano-Maciá M, Martinez-Chantar ML, Avila MA, Aspichueta P, Calvisi DF, Evert M, Fabris L, Castro RE, Elortza F, Andersen JB, Bujanda L, Rodrigues PM, Perugorria MJ, Banales JM. Targeting NAE1-mediated protein hyper-NEDDylation halts cholangiocarcinogenesis and impacts on tumor-stroma crosstalk in experimental models. J Hepatol 2022; 77:177-190. [PMID: 35217064 DOI: 10.1016/j.jhep.2022.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 06/15/2021] [Revised: 01/13/2022] [Accepted: 02/08/2022] [Indexed: 12/04/2022]
Abstract
BACKGROUND & AIMS Cholangiocarcinoma (CCA) comprises a heterogeneous group of malignant tumors associated with dismal prognosis. Alterations in post-translational modifications (PTMs), including NEDDylation, result in abnormal protein dynamics, cell disturbances and disease. Herein, we investigate the role of NEDDylation in CCA development and progression. METHODS Levels and functions of NEDDylation, together with response to pevonedistat (NEDDylation inhibitor) or CRISPR/Cas9 against NAE1 were evaluated in vitro, in vivo and/or in patients with CCA. The development of preneoplastic lesions in Nae1+/- mice was investigated using an oncogene-driven CCA model. The impact of NEDDylation in CCA cells on tumor-stroma crosstalk was assessed using CCA-derived cancer-associated fibroblasts (CAFs). Proteomic analyses were carried out by mass-spectrometry. RESULTS The NEDDylation machinery was found overexpressed and overactivated in human CCA cells and tumors. Most NEDDylated proteins found upregulated in CCA cells, after NEDD8-immunoprecipitation and further proteomics, participate in the cell cycle, proliferation or survival. Genetic (CRISPR/Cas9-NAE1) and pharmacological (pevonedistat) inhibition of NEDDylation reduced CCA cell proliferation and impeded colony formation in vitro. NEDDylation depletion (pevonedistat or Nae1+/- mice) halted tumorigenesis in subcutaneous, orthotopic, and oncogene-driven models of CCA in vivo. Moreover, pevonedistat potentiated chemotherapy-induced cell death in CCA cells in vitro. Mechanistically, impaired NEDDylation triggered the accumulation of both cullin RING ligase and NEDD8 substrates, inducing DNA damage and cell cycle arrest. Furthermore, impaired NEDDylation in CCA cells reduced the secretion of proteins involved in fibroblast activation, angiogenesis, and oncogenic pathways, ultimately hampering CAF proliferation and migration. CONCLUSION Aberrant protein NEDDylation contributes to cholangiocarcinogenesis by promoting cell survival and proliferation. Moreover, NEDDylation impacts the CCA-stroma crosstalk. Inhibition of NEDDylation with pevonedistat may represent a potential therapeutic strategy for patients with CCA. LAY SUMMARY Little is known about the role of post-translational modifications of proteins in cholangiocarcinoma development and progression. Herein, we show that protein NEDDylation is upregulated and hyperactivated in cholangiocarcinoma, promoting tumor growth. Pharmacological inhibition of NEDDylation halts cholangiocarcinogenesis and could be an effective therapeutic strategy to tackle these tumors.
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Affiliation(s)
- Paula Olaizola
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital -, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Pui Yuen Lee-Law
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital -, University of the Basque Country (UPV/EHU), San Sebastian, Spain; Department of Gastroenterology & Hepatology, Radboud University Nijmegen Medical Center, The Netherlands
| | - Maite G Fernandez-Barrena
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; Hepatology Program, CIMA. University of Navarra, Pamplona, Spain; Instituto de Investigaciones Sanitarias de Navarra (IdiSNA), Pamplona, Spain
| | - Laura Alvarez
- Hepatology Program, CIMA. University of Navarra, Pamplona, Spain
| | | | - Mikel Azkargorta
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), ProteoRed-ISCIII, Bizkaia Science and Technology Park, Derio, Spain
| | - Colm J O'Rourke
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Francisco J Caballero-Camino
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital -, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Irene Olaizola
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital -, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Rocio I R Macias
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; Experimental Hepatology and Drug Targeting (HEVEPHARM) Group, Institute of Biomedical Research of Salamanca (IBSAL), University of Salamanca, Salamanca, Spain
| | - Jose J G Marin
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; Experimental Hepatology and Drug Targeting (HEVEPHARM) Group, Institute of Biomedical Research of Salamanca (IBSAL), University of Salamanca, Salamanca, Spain
| | - Marina Serrano-Maciá
- Liver Disease Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Spain
| | - Maria L Martinez-Chantar
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; Liver Disease Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Spain
| | - Matias A Avila
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; Hepatology Program, CIMA. University of Navarra, Pamplona, Spain; Instituto de Investigaciones Sanitarias de Navarra (IdiSNA), Pamplona, Spain
| | - Patricia Aspichueta
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; Biocruces Bizkaia Health Research Institute, Cruces University Hospital, 48903 Barakaldo, Spain
| | - Diego F Calvisi
- Institute of Pathology, University of Regensburg, Regensburg, Germany
| | - Matthias Evert
- Institute of Pathology, University of Regensburg, Regensburg, Germany
| | - Luca Fabris
- Department of Molecular Medicine (DMM), University of Padua, Padua, Italy; Department of Internal Medicine, Yale Liver Center (YLC), School of Medicine, Yale University New Haven, CT, USA
| | - Rui E Castro
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Felix Elortza
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), ProteoRed-ISCIII, Bizkaia Science and Technology Park, Derio, Spain
| | - Jesper B Andersen
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Luis Bujanda
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health 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
| | - Pedro M Rodrigues
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health 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, Bilbao, Spain.
| | - Maria J Perugorria
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health 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; Department of Medicine, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain.
| | - Jesus M Banales
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health 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, Bilbao, Spain; Department of Biochemistry and Genetics, School of Sciences, University of Navarra, Pamplona, Spain.
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20
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Auzmendi-Iriarte J, Otaegi-Ugartemendia M, Carrasco-Garcia E, Azkargorta M, Diaz A, Saenz-Antoñanzas A, Andermatten JA, Garcia-Puga M, Garcia I, Elua-Pinin A, Ruiz I, Sampron N, Elortza F, Cuervo AM, Matheu A. Chaperone-Mediated Autophagy Controls Proteomic and Transcriptomic Pathways to Maintain Glioma Stem Cell Activity. Cancer Res 2022; 82:1283-1297. [PMID: 35131870 PMCID: PMC9359743 DOI: 10.1158/0008-5472.can-21-2161] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 12/15/2021] [Accepted: 01/27/2022] [Indexed: 02/07/2023]
Abstract
Chaperone-mediated autophagy (CMA) is a homeostatic process essential for the lysosomal degradation of a selected subset of the proteome. CMA activity directly depends on the levels of LAMP2A, a critical receptor for CMA substrate proteins at the lysosomal membrane. In glioblastoma (GBM), the most common and aggressive brain cancer in adulthood, high levels of LAMP2A in the tumor and tumor-associated pericytes have been linked to temozolomide resistance and tumor progression. However, the role of LAMP2A, and hence CMA, in any cancer stem cell type or in glioblastoma stem cells (GSC) remains unknown. In this work, we show that LAMP2A expression is enriched in patient-derived GSCs, and its depletion diminishes GSC-mediated tumorigenic activities. Conversely, overexpression of LAMP2A facilitates the acquisition of GSC properties. Proteomic and transcriptomic analysis of LAMP2A-depleted GSCs revealed reduced extracellular matrix interaction effectors in both analyses. Moreover, pathways related to mitochondrial metabolism and the immune system were differentially deregulated at the proteome level. Furthermore, clinical samples of GBM tissue presented overexpression of LAMP2, which correlated with advanced glioma grade and poor overall survival. In conclusion, we identified a novel role of CMA in directly regulating GSCs activity via multiple pathways at the proteome and transcriptome levels. SIGNIFICANCE A receptor of chaperone-mediated autophagy regulates glioblastoma stem cells and may serve as a potential biomarker for advanced tumor grade and poor survival in this disease.
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Affiliation(s)
| | | | | | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, ProteoRed-ISCIII, Spain
| | - Antonio Diaz
- Department of Development and Molecular Biology, Albert Einstein College of Medicine, Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, New York
| | | | | | - Mikel Garcia-Puga
- Cellular Oncology Group, Biodonostia Health Research Institute, San Sebastian, Spain
| | - Idoia Garcia
- Cellular Oncology Group, Biodonostia Health Research Institute, San Sebastian, Spain
| | | | - Irune Ruiz
- Cellular Oncology Group, Biodonostia Health Research Institute, San Sebastian, Spain.,Donostia University Hospital, Osakidetza, San Sebastian, Spain
| | - Nicolas Sampron
- Cellular Oncology Group, Biodonostia Health Research Institute, San Sebastian, Spain.,Donostia University Hospital, Osakidetza, San Sebastian, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, ProteoRed-ISCIII, Spain
| | - Ana Maria Cuervo
- Department of Development and Molecular Biology, Albert Einstein College of Medicine, Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, New York
| | - Ander Matheu
- Cellular Oncology Group, Biodonostia Health Research Institute, San Sebastian, Spain.,CIBER de Fragilidad y Envejecimiento Saludable (CIBERfes), Madrid, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.,Corresponding Author: Ander Matheu, Cellular Oncology, Biodonostia Health Research Institute, Paseo Dr. Beguiristain s/n, San Sebastian 20014, Spain. E-mail:
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21
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Pilar-Orive FJ, Astigarraga I, Azkargorta M, Elortza F, Garcia-Obregon S. A Three-Protein Panel to Support the Diagnosis of Sepsis in Children. J Clin Med 2022; 11:jcm11061563. [PMID: 35329889 PMCID: PMC8955185 DOI: 10.3390/jcm11061563] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/07/2022] [Accepted: 03/10/2022] [Indexed: 02/01/2023] Open
Abstract
Sepsis is a syndrome without a standard validated diagnostic test. Early recognition is crucial. Serum proteome analysis in children with sepsis may identify new biomarkers. This study aimed to find suitable blood biomarkers for an early diagnosis of sepsis. An analytical observational case-control study was carried out in a single center. Children admitted to a Pediatric Intensive Care Unit with clinical diagnosed sepsis were eligible for study. A proteomic analysis conducted by mass spectrometry was performed. Forty patients with sepsis and 24 healthy donors were recruited. Proteomics results revealed 44 proteins differentially expressed between patients and healthy controls. Six proteins were selected to be validated: lactoferrin, serum amyloid-A1 (SAA-1), complement factor B, leucine-rich alpha-2 glycoprotein (LRG1), soluble interleukin-2 alpha chain receptor (sCD25) and soluble haptoglobin−hemoglobin receptor. Our results showed that sCD25, SAA-1, and LRG1 had high levels of specificity and sensitivity, as well as an excellent area under the ROC curve (>0.9). Our study provides a serum proteomic analysis that identifies new diagnostic biomarkers in sepsis. SAA-1, sCD25 and LRG1 were able to separate septic from healthy donor, so they could be used together with other clinical and analytical features to improve sepsis diagnosis in children.
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Affiliation(s)
- Francisco J. Pilar-Orive
- Pediatric Critical Care Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- Pediatric Critical Care Service, Hospital Universitario Cruces, 48903 Barakaldo, Spain
- Correspondence: (F.J.P.-O.); (S.G.-O.); Tel.: +34-616958309 (F.J.P.-O.); +34-946006357 (S.G.-O.)
| | - Itziar Astigarraga
- Pediatric Oncology Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Pediatric Service, Hospital Universitario Cruces, 48903 Barakaldo, Spain
- Pediatric Department, Universidad del País Vasco UPV/EHU, 48940 Leioa, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain; (M.A.); (F.E.)
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain; (M.A.); (F.E.)
| | - Susana Garcia-Obregon
- Pediatric Oncology Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Physiology Department, Universidad del País Vasco UPV/EHU, 48940 Leioa, Spain
- Correspondence: (F.J.P.-O.); (S.G.-O.); Tel.: +34-616958309 (F.J.P.-O.); +34-946006357 (S.G.-O.)
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22
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Colomé N, Abian J, Aloria K, Arizmendi JM, Barceló-Batllori S, Braga-Lagache S, Burlet-Schiltz O, Carrascal M, Casal JI, Chicano-Gálvez E, Chiva C, Clemente LF, Elortza F, Estanyol JM, Fernandez-Irigoyen J, Fernández-Puente P, Fidalgo MJ, Froment C, Fuentes M, Fuentes-Almagro C, Gay M, Hainard A, Heller M, Hernández ML, Ibarrola N, Iloro I, Kieselbach T, Lario A, Locard-Paulet M, Marina-Ramírez A, Martín L, Morato-López E, Muñoz J, Navajas R, Odena MA, Odriozola L, de Oliveira E, Paradela A, Pasquarello C, de Los Rios V, Ruiz-Romero C, Sabidó E, Sánchez Del Pino M, Sancho J, Santamaría E, Schaeffer-Reiss C, Schneider J, de la Torre C, Valero ML, Vilaseca M, Wu S, Wu L, Ximénez de Embún P, Canals F, Corrales FJ. Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis. J Proteomics 2022; 251:104409. [PMID: 34758407 DOI: 10.1016/j.jprot.2021.104409] [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: 10/01/2021] [Revised: 10/12/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022]
Abstract
Global analysis of protein phosphorylation by mass spectrometry proteomic techniques has emerged in the last decades as a powerful tool in biological and biomedical research. However, there are several factors that make the global study of the phosphoproteome more challenging than measuring non-modified proteins. The low stoichiometry of the phosphorylated species and the need to retrieve residue specific information require particular attention on sample preparation, data acquisition and processing to ensure reproducibility, qualitative and quantitative robustness and ample phosphoproteome coverage in phosphoproteomic workflows. Aiming to investigate the effect of different variables in the performance of proteome wide phosphoprotein analysis protocols, ProteoRed-ISCIII and EuPA launched the Proteomics Multicentric Experiment 11 (PME11). A reference sample consisting of a yeast protein extract spiked in with different amounts of a phosphomix standard (Sigma/Merck) was distributed to 31 laboratories around the globe. Thirty-six datasets from 23 laboratories were analyzed. Our results indicate the suitability of the PME11 reference sample to benchmark and optimize phosphoproteomics strategies, weighing the influence of different factors, as well as to rank intra and inter laboratory performance.
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Affiliation(s)
- Núria Colomé
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain
| | - Joaquín Abian
- ProteoRed-ISCIII, Instituto de Investigaciones Biomédicas de Barcelona, IIBB-CSIC/IDIBAPS, 08036 Barcelona, Spain
| | - Kerman Aloria
- ProteoRed-ISCIII, Proteomics Core Facility-SGIKER, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Jesús M Arizmendi
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | | | - Sophie Braga-Lagache
- Department for BioMedical Research (DBMR), Proteomics and Mass Spectrometry Core Facility, University of Bern, CH-3010 Bern, Switzerland
| | - Odile Burlet-Schiltz
- Proteomics and Mass Spectrometry of Biomolecules, Proteomics Infrastructure of Toulouse, Proteomics French Infrastructure, ProFI. Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, UPS, CNRS, Toulouse, France
| | - Montse Carrascal
- ProteoRed-ISCIII, Instituto de Investigaciones Biomédicas de Barcelona, IIBB-CSIC/IDIBAPS, 08036 Barcelona, Spain
| | - J Ignacio Casal
- ProteoRed-ISCIII, Centro de Investigaciones Biológicas-CSIC, Madrid 28040, Spain
| | - Eduard Chicano-Gálvez
- ProteoRed-ISCIII, Proteomics Unit, IMIBIC/UCO/HURS, IMIBIC Building Fl.3, 14004 Córdoba, Spain
| | - Cristina Chiva
- Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; ProteoRed ISCIII, Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Felix Elortza
- ProteoRed-ISCIII, CIC bioGUNE, Proteomics Platform, Basque Research & Technology Alliance (BRTA), CIBERehd,Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Josep M Estanyol
- ProteoRed-ISCIII, Scientific and Technological Centers (CCiTUB), University of Barcelona, 08036 Barcelona, Spain
| | - Joaquín Fernandez-Irigoyen
- Proteored-ISCIII. Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, 31008 Pamplona, Spain
| | - Patricia Fernández-Puente
- Grupo de Investigación de Reumatología (GIR), Agrupación CICA-INIBIC, Universidad de A Coruña, A Coruña, Spain
| | - María José Fidalgo
- ProteoRed-ISCIII, Scientific and Technological Centers (CCiTUB), University of Barcelona, 08036 Barcelona, Spain
| | - Carine Froment
- Proteomics and Mass Spectrometry of Biomolecules, Proteomics Infrastructure of Toulouse, Proteomics French Infrastructure, ProFI. Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, UPS, CNRS, Toulouse, France
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Proteomics Unit, CIBERONC, Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), Universidad de Salamanca, Spain
| | - Carlos Fuentes-Almagro
- Proteomics Unit, SCAI, University of Córdoba, Ramón y Cajal Building, Rabanales Campus, 14071, Córdoba, Spain
| | - Marina Gay
- ProteoRed-ISCIII, Institute for Research in Biomedicine (IRB Barcelona), BIST (The Barcelona Institute of Science and Technology), Baldiri i Reixac 10, 08028 Barcelona, Spain
| | | | - Manfred Heller
- Department for BioMedical Research (DBMR), Proteomics and Mass Spectrometry Core Facility, University of Bern, CH-3010 Bern, Switzerland
| | | | - Nieves Ibarrola
- ProteoRed-ISCIII, Proteomics Unit. Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), Universidad de Salamanca-CSIC, Salamanca, Spain
| | - Ibon Iloro
- ProteoRed-ISCIII, CIC bioGUNE, Proteomics Platform, Basque Research & Technology Alliance (BRTA), CIBERehd,Bizkaia Science and Technology Park, 48160 Derio, Spain
| | | | | | - Marie Locard-Paulet
- Proteomics and Mass Spectrometry of Biomolecules, Proteomics Infrastructure of Toulouse, Proteomics French Infrastructure, ProFI. Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, UPS, CNRS, Toulouse, France
| | | | - Luna Martín
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain
| | | | - Javier Muñoz
- ProteoRed-ISCIII, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Rosana Navajas
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain
| | - M Antonia Odena
- ProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, 08028, Barcelona, Spain
| | - Leticia Odriozola
- ProteoRed-ISCIII, CIMA, University of Navarra, 31008, Pamplona, Spain
| | - Eliandre de Oliveira
- ProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, 08028, Barcelona, Spain
| | - Alberto Paradela
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain
| | | | - Vivian de Los Rios
- ProteoRed-ISCIII, Centro de Investigaciones Biológicas-CSIC, Madrid 28040, Spain
| | - Cristina Ruiz-Romero
- Grupo de Investigación de Reumatología (GIR) - ProteoRed-ISCIII, Unidad de Proteómica, INIBIC-Complejo Hospitalario Universitario de A Coruña, SERGAS, A Coruña, Spain
| | - Eduard Sabidó
- Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; ProteoRed ISCIII, Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Manuel Sánchez Del Pino
- Biotechnology and Biomedicine Interdisciplinary Research Unit (ERI BIOTECMED), University of Valencia, 46100 Burjassot, Spain
| | - Jaime Sancho
- ProteoRed-ISCIII, IPBLN -CSIC, 18016 Granada, Spain
| | - Enrique Santamaría
- Proteored-ISCIII. Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, 31008 Pamplona, Spain
| | - Christine Schaeffer-Reiss
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
| | - Justine Schneider
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
| | - Carolina de la Torre
- ProteoRed-ISCIII, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - M Luz Valero
- ProteoRed-ISCIII, Proteomics Unit, Central Service for Experimental Research (SCSIE), University of Valencia, 46100, Burjassot, Spain
| | - Marta Vilaseca
- ProteoRed-ISCIII, Institute for Research in Biomedicine (IRB Barcelona), BIST (The Barcelona Institute of Science and Technology), Baldiri i Reixac 10, 08028 Barcelona, Spain
| | - Shuai Wu
- Agilent Technologies, Inc., Santa Clara, CA 95051, USA
| | - Linfeng Wu
- Agilent Technologies, Inc., Santa Clara, CA 95051, USA
| | | | - Francesc Canals
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain.
| | - Fernando J Corrales
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain; ProteoRed-ISCIII, CIMA, University of Navarra, 31008, Pamplona, Spain.
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- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain; ProteoRed-ISCIII-PRB3, Spanish Proteomics Networked Platform, Centro Nacional de Biotecnología (CSIC), 28049, Madrid, Spain
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- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain; European Proteomics Association, Standardization Initiative, , Centro Nacional de Biotecnología (CSIC), 28049, Madrid, Spain
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23
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Acera A, Gómez-Esteban JC, Murueta-Goyena A, Galdos M, Azkargorta M, Elortza F, Ruzafa N, Ibarrondo O, Pereiro X, Vecino E. Potential Tear Biomarkers for the Diagnosis of Parkinson’s Disease—A Pilot Study. Proteomes 2022; 10:proteomes10010004. [PMID: 35076620 PMCID: PMC8788479 DOI: 10.3390/proteomes10010004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/09/2022] [Accepted: 01/10/2022] [Indexed: 11/17/2022] Open
Abstract
Parkinson’s disease (PD) is the second most common neurodegenerative disease after Alzheimer’s disease. In this study, the tear proteome profile of patients with idiopathic PD (iPD, n = 24), carriers of the E46K-SNCA mutation (n = 3) and healthy control (CT, n = 27) subjects was analyzed to identify candidate biomarkers for the diagnosis of PD. An observational, prospective and case-control pilot study was carried out, analyzing the participants tear samples by nano-liquid chromatography–mass spectrometry (nLC–MS/MS) and assessing their neurological impairment. The proteomic data obtained are available at ProteomeXchange with identifier 10.6019/PXD028811. These analyses led to the identification of 560 tear proteins, some of which were deregulated in PD patients and that have been implicated in immune responses, inflammation, apoptosis, collagen degradation, protein synthesis, defense, lipid transport and altered lysosomal function. Of these proteins, six were related to neurodegenerative processes and showed a good capacity to classify patients and controls. These findings revealed that certain proteins were upregulated in the tears of PD patients, mainly proteins involved in lysosomal function. Thus, in this study, tear proteins were identified that are implicated in neurodegeneration and that may be related to an aggressive disease phenotype in PD patients.
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Affiliation(s)
- Arantxa Acera
- Experimental Ophthalmo-Biology Group, Department of Cell Biology and Histology, University of the Basque Country UPV/EHU, 48940 Leioa, Spain; (A.A.); (N.R.); (X.P.)
- Department of Neuroscience, Biodonostia Health Research Institute, 20014 Donostia-San Sebastian, Spain
| | - Juan Carlos Gómez-Esteban
- Department of Neurology, Cruces University Hospital, 48903 Barakaldo, Spain;
- Neurodegenerative Diseases Group, BioCruces Health Research Institute, 48903 Barakaldo, Spain;
- Department of Neurosciences, Faculty of Medicine and Nursery, University of the Basque Country UPV/EHU, 48940 Leioa, Spain
| | - Ane Murueta-Goyena
- Neurodegenerative Diseases Group, BioCruces Health Research Institute, 48903 Barakaldo, Spain;
- Department of Neurosciences, Faculty of Medicine and Nursery, University of the Basque Country UPV/EHU, 48940 Leioa, Spain
| | - Marta Galdos
- Begiker-Ophthalmology Research Group, BioCruces Health Research Institute, 48903 Barakaldo, Spain;
| | - Mikel Azkargorta
- Department of Proteomics, Center for Cooperative Research in Biosciences, 48160 Derio, Spain; (M.A.); (F.E.)
| | - Felix Elortza
- Department of Proteomics, Center for Cooperative Research in Biosciences, 48160 Derio, Spain; (M.A.); (F.E.)
| | - Noelia Ruzafa
- Experimental Ophthalmo-Biology Group, Department of Cell Biology and Histology, University of the Basque Country UPV/EHU, 48940 Leioa, Spain; (A.A.); (N.R.); (X.P.)
- Begiker-Ophthalmology Research Group, BioCruces Health Research Institute, 48903 Barakaldo, Spain;
| | | | - Xandra Pereiro
- Experimental Ophthalmo-Biology Group, Department of Cell Biology and Histology, University of the Basque Country UPV/EHU, 48940 Leioa, Spain; (A.A.); (N.R.); (X.P.)
- Begiker-Ophthalmology Research Group, BioCruces Health Research Institute, 48903 Barakaldo, Spain;
| | - Elena Vecino
- Experimental Ophthalmo-Biology Group, Department of Cell Biology and Histology, University of the Basque Country UPV/EHU, 48940 Leioa, Spain; (A.A.); (N.R.); (X.P.)
- Begiker-Ophthalmology Research Group, BioCruces Health Research Institute, 48903 Barakaldo, Spain;
- Correspondence: ; Tel.: +34-94-601-2820
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24
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Escobés I, Azkargorta M, Iloro I, Elortza F. Differential Proteomic Analysis of Complex Mixtures by Label-Free nLC MS/MS. Methods Mol Biol 2022; 2471:111-121. [PMID: 35175593 DOI: 10.1007/978-1-0716-2193-6_5] [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] [Indexed: 06/14/2023]
Abstract
After over two decades of constant evolution, proteomics can be truly considered nowadays as a high-throughput technique. Latest advances performed in sample preparation, instrumentation, and data analysis tools enable proteome-wide detection and quantification of proteins in complex samples.Label-free quantification by nanoscale liquid chromatography coupled online to tandem mass spectrometry (nLC MS /MS ) is a straightforward procedure for relative protein quantification. This approach allows to get deeper insights of what molecular changes are involved in the biological system we want to study in an unbiased manner.This chapter describes methods for sample preparation prior to mass spectrometry analysis. Besides, we describe a standard acquisition method, and some common bioinformatics analyses that help extracting biologically relevant information out of the achieved data.
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Affiliation(s)
- Iraide Escobés
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), ProteoRed-ISCIII, CIBERehd, Science and Technology Park of Bizkaia, Derio, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), ProteoRed-ISCIII, CIBERehd, Science and Technology Park of Bizkaia, Derio, Spain
| | - Ibon Iloro
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), ProteoRed-ISCIII, CIBERehd, Science and Technology Park of Bizkaia, Derio, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), ProteoRed-ISCIII, CIBERehd, Science and Technology Park of Bizkaia, Derio, Spain.
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25
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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.
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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
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Anitua E, Muruzabal F, Pino A, Prado R, Azkargorta M, Elortza F, Merayo-Lloves J. Proteomic Characterization of Plasma Rich in Growth Factors and Undiluted Autologous Serum. Int J Mol Sci 2021; 22:ijms222212176. [PMID: 34830053 PMCID: PMC8618701 DOI: 10.3390/ijms222212176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/03/2021] [Accepted: 11/09/2021] [Indexed: 12/21/2022] Open
Abstract
Over the last three decades, there has been special interest in developing drugs that mimic the characteristics of natural tears for use it in the treatment of several ocular surface disorders. Interestingly, the composition of blood plasma is very similar to tears. Therefore, different blood-derived products like autologous serum (AS) and plasma rich in growth factors (PRGF) have been developed for the treatment of diverse ocular pathologies. However, scarce studies have been carried out to analyze the differences between both types of blood-derived products. In the present study, blood from three healthy donors was drawn and processed to obtain AS and PRGF eye drops. Then, human corneal stromal keratocytes (HK) were treated with PRGF or undiluted AS. Proteomic analysis was carried out to analyze and characterize the differential protein profiles between PRGF and AS, and the differentially expressed proteins in HK cells after PRGF and AS treatment. The results obtained in the present study show that undiluted AS induces the activation of different pathways related to an inflammatory, angiogenic, oxidative stress and scarring response in HK cells regarding PRGF. These results suggest that PRGF could be a better alternative than AS for the treatment of ocular surface disorders.
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Affiliation(s)
- Eduardo Anitua
- BTI—Biotechnology Institute, 01007 Vitoria, Spain; (F.M.); (A.P.); (R.P.)
- University Institute for Regenerative Medicine and Oral Implantology—UIRMI (UPV/EHU-Fundación Eduardo Anitua), 01007 Vitoria, Spain
- Correspondence:
| | - Francisco Muruzabal
- BTI—Biotechnology Institute, 01007 Vitoria, Spain; (F.M.); (A.P.); (R.P.)
- University Institute for Regenerative Medicine and Oral Implantology—UIRMI (UPV/EHU-Fundación Eduardo Anitua), 01007 Vitoria, Spain
| | - Ander Pino
- BTI—Biotechnology Institute, 01007 Vitoria, Spain; (F.M.); (A.P.); (R.P.)
- University Institute for Regenerative Medicine and Oral Implantology—UIRMI (UPV/EHU-Fundación Eduardo Anitua), 01007 Vitoria, Spain
| | - Roberto Prado
- BTI—Biotechnology Institute, 01007 Vitoria, Spain; (F.M.); (A.P.); (R.P.)
- University Institute for Regenerative Medicine and Oral Implantology—UIRMI (UPV/EHU-Fundación Eduardo Anitua), 01007 Vitoria, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain; (M.A.); (F.E.)
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain; (M.A.); (F.E.)
| | - Jesús Merayo-Lloves
- Instituto Oftalmológico Fernández-Vega, Fundación de Investigación Oftalmológica, Universidad de Oviedo, 33012 Oviedo, Spain;
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Echave M, Erezuma I, Golafshan N, Castilho M, Kadumudi F, Pimenta-Lopes C, Ventura F, Pujol A, Jimenez J, Camara J, Hernáez-Moya R, Iturriaga L, Sáenz Del Burgo L, Iloro I, Azkargorta M, Elortza F, Lakshminarayanan R, Al-Tel T, García-García P, Reyes R, Delgado A, Évora C, Pedraz J, Dolatshahi-Pirouz A, Orive G. Bioinspired gelatin/bioceramic composites loaded with bone morphogenetic protein-2 (BMP-2) promote osteoporotic bone repair. Materials Science and Engineering: C 2021; 134:112539. [DOI: 10.1016/j.msec.2021.112539] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 12/17/2022]
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28
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Azkargorta M, Iloro I, Escobes I, Cabrera D, Falcon-Perez JM, Elortza F, Royo F. Human Serum Extracellular Vesicle Proteomic Profile Depends on the Enrichment Method Employed. Int J Mol Sci 2021; 22:ijms222011144. [PMID: 34681804 PMCID: PMC8540106 DOI: 10.3390/ijms222011144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/10/2021] [Accepted: 10/13/2021] [Indexed: 12/16/2022] Open
Abstract
The proteomic profiling of serum samples supposes a challenge due to the large abundance of a few blood proteins in comparison with other circulating proteins coming from different tissues and cells. Although the sensitivity of protein detection has increased enormously in the last years, specific strategies are still required to enrich less abundant proteins and get rid of abundant proteins such as albumin, lipoproteins, and immunoglobulins. One of the alternatives that has become more promising is to characterize circulating extracellular vesicles from serum samples that have great interest in biomedicine. In the present work, we enriched the extracellular vesicles fraction from human serum by applying different techniques, including ultracentrifugation, size-exclusion chromatography, and two commercial precipitation methods based on different mechanisms of action. To improve the performance and efficacy of the techniques to promote purity of the preparations, we have employed a small volume of serum samples (<100 mL). The comparative proteomic profiling of the enriched preparations shows that ultracentrifugation procedure yielded a larger and completely different set of proteins than other techniques, including mitochondrial and ribosome related proteins. The results showed that size exclusion chromatography carries over lipoprotein associated proteins, while a polymer-based precipitation kit has more affinity for proteins associated with granules of platelets. The precipitation kit that targets glycosylation molecules enriches differentially protein harboring glycosylation sites, including immunoglobulins and proteins of the membrane attack complex.
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Affiliation(s)
- Mikel Azkargorta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
| | - Ibon Iloro
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
| | - Iraide Escobes
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
| | - Diana Cabrera
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
| | - Juan M. Falcon-Perez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
- Network Center of Cooperative Research in Biomedicine of Hepatic and Digestive Diseases (CIBERehd), 28029 Madrid, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Felix Elortza
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
- Network Center of Cooperative Research in Biomedicine of Hepatic and Digestive Diseases (CIBERehd), 28029 Madrid, Spain
- Correspondence: (F.E.); (F.R.)
| | - Felix Royo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
- Network Center of Cooperative Research in Biomedicine of Hepatic and Digestive Diseases (CIBERehd), 28029 Madrid, Spain
- Correspondence: (F.E.); (F.R.)
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Lee-Law PY, Olaizola P, Caballero-Camino FJ, Izquierdo-Sanchez L, Rodrigues PM, Perugorria MJ, Azkargorta M, Elortza F, Martinez-Chantar ML, Aspichueta P, Marzioni M, Bujanda L, Drenth JPH, Banales JM. Inhibition of NAE-dependent protein hyper-NEDDylation in cystic cholangiocytes halts cystogenesis in experimental models of polycystic liver disease. United European Gastroenterol J 2021; 9:848-859. [PMID: 34310849 PMCID: PMC8435261 DOI: 10.1002/ueg2.12126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 04/01/2021] [Indexed: 12/23/2022] Open
Abstract
Background Polycystic liver diseases (PLDs) are genetic inherited disorders characterized by the progressive growth of numerous intrahepatic biliary cysts, which are the main cause of morbidity. Previous studies revealed that cystic cholangiocytes are characterized by endoplasmic reticulum stress and aberrant posttranslational modification (PTM) of proteins, in particular hyper‐SUMOylation, that promote PLD pathobiology. Protein NEDDylation is a newly characterized PTM that modulates a plethora of biological processes and its dysregulation is associated with the development and progression of several human diseases. However, the role of NEDDylation in PLD remains elusive. Objective To explore the role of protein NEDDylation in PLD and its potential therapeutic regulatory value. Methods Levels and functional effects of NEDDylation, including response to Pevonedistat (first‐in‐class selective inhibitor of the NEDDylation E1 enzyme NAE), were assessed in vitro, in vivo, and/or in patients with PLD. NEDDylated protein levels in normal and cystic human cholangiocytes were assessed by immunoprecipitation, and the proteomic profile was further analyzed by mass spectrometry. Results and Conclusion The genes involved in the NEDDylation pathway were found overexpressed (mRNA) in polycystic human and rat liver tissue, as well as in cystic cholangiocytes in culture, compared to controls. Elevated levels of NEDDylated proteins were further confirmed in cystic cholangiocytes in vitro, which diminished under Pevonedistat incubation. Pevonedistat promoted apoptotic cell death and reduced proliferation in cystic cholangiocytes in vitro. Comparative proteomic profiling of NEDD8‐immunoprecipitated proteins between normal and cystic cholangiocytes in culture reported candidate proteins involved in cystogenesis, mostly associated with protein biogenesis and quality control. All these data indicate that cystic cholangiocytes display increased protein NEDDylation, contributing to cell survival and proliferation, ultimately supporting hepatic cystogenesis. Targeting of protein hyper‐NEDDylation in cystic cholangiocytes inhibits cystogenesis in experimental models, representing a novel therapeutic opportunity in PLD.
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Affiliation(s)
- Pui Y Lee-Law
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute-Donostia University Hospital, University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain.,Department of Gastroenterology & Hepatology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Paula Olaizola
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute-Donostia University Hospital, University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain
| | - Francisco J Caballero-Camino
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute-Donostia University Hospital, University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain
| | - Laura Izquierdo-Sanchez
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute-Donostia University Hospital, University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain.,National Institute for the Study of Liver and Gastrointestinal Diseases, (CIBERehd, "Instituto de Salud Carlos III"), Madrid, Spain
| | - Pedro M Rodrigues
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute-Donostia University Hospital, University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain.,National Institute for the Study of Liver and Gastrointestinal Diseases, (CIBERehd, "Instituto de Salud Carlos III"), Madrid, Spain
| | - Maria J Perugorria
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute-Donostia University Hospital, University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain.,National Institute for the Study of Liver and Gastrointestinal Diseases, (CIBERehd, "Instituto de Salud Carlos III"), Madrid, Spain
| | - Mikel Azkargorta
- National Institute for the Study of Liver and Gastrointestinal Diseases, (CIBERehd, "Instituto de Salud Carlos III"), Madrid, Spain.,Proteomics Platform, CIC bioGUNE, ProteoRed-ISCIII, Bizkaia Science and Technology Park, Derio, Spain
| | - Felix Elortza
- National Institute for the Study of Liver and Gastrointestinal Diseases, (CIBERehd, "Instituto de Salud Carlos III"), Madrid, Spain.,Proteomics Platform, CIC bioGUNE, ProteoRed-ISCIII, Bizkaia Science and Technology Park, Derio, Spain
| | - Maria L Martinez-Chantar
- National Institute for the Study of Liver and Gastrointestinal Diseases, (CIBERehd, "Instituto de Salud Carlos III"), Madrid, Spain.,Liver Disease Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Patricia Aspichueta
- Department of Physiology, Faculty of Medicine and Nursing, UPV/EHU, Leioa, Spain.,Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain
| | - Marco Marzioni
- Department of Gastroenterology, Università Politecnica delle Marche, Ancona, Italy
| | - Luis Bujanda
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute-Donostia University Hospital, University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain.,National Institute for the Study of Liver and Gastrointestinal Diseases, (CIBERehd, "Instituto de Salud Carlos III"), Madrid, Spain
| | - Joost P H Drenth
- Department of Gastroenterology & Hepatology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Jesus M Banales
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute-Donostia University Hospital, University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain.,National Institute for the Study of Liver and Gastrointestinal Diseases, (CIBERehd, "Instituto de Salud Carlos III"), Madrid, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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30
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Esparza-Baquer A, Labiano I, Sharif O, Agirre-Lizaso A, Oakley F, Rodrigues PM, Zhuravleva E, O'Rourke CJ, Hijona E, Jimenez-Agüero R, Riaño I, Landa A, La Casta A, Zaki MYW, Munoz-Garrido P, Azkargorta M, Elortza F, Vogel A, Schabbauer G, Aspichueta P, Andersen JB, Knapp S, Mann DA, Bujanda L, Banales JM, Perugorria MJ. TREM-2 defends the liver against hepatocellular carcinoma through multifactorial protective mechanisms. Gut 2021; 70:1345-1361. [PMID: 32907830 PMCID: PMC8223629 DOI: 10.1136/gutjnl-2019-319227] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Hepatocellular carcinoma (HCC) is a prevalent and aggressive cancer usually arising on a background of chronic liver injury involving inflammatory and hepatic regenerative processes. The triggering receptor expressed on myeloid cells 2 (TREM-2) is predominantly expressed in hepatic non-parenchymal cells and inhibits Toll-like receptor signalling, protecting the liver from various hepatotoxic injuries, yet its role in liver cancer is poorly defined. Here, we investigated the impact of TREM-2 on liver regeneration and hepatocarcinogenesis. DESIGN TREM-2 expression was analysed in liver tissues of two independent cohorts of patients with HCC and compared with control liver samples. Experimental HCC and liver regeneration models in wild type and Trem-2-/- mice, and in vitro studies with hepatic stellate cells (HSCs) and HCC spheroids were conducted. RESULTS TREM-2 expression was upregulated in human HCC tissue, in mouse models of liver regeneration and HCC. Trem-2-/- mice developed more liver tumours irrespective of size after diethylnitrosamine (DEN) administration, displayed exacerbated liver damage, inflammation, oxidative stress and hepatocyte proliferation. Administering an antioxidant diet blocked DEN-induced hepatocarcinogenesis in both genotypes. Similarly, Trem-2-/- animals developed more and larger tumours in fibrosis-associated HCC models. Trem-2-/- livers showed increased hepatocyte proliferation and inflammation after partial hepatectomy. Conditioned media from human HSCs overexpressing TREM-2 inhibited human HCC spheroid growth in vitro through attenuated Wnt ligand secretion. CONCLUSION TREM-2 plays a protective role in hepatocarcinogenesis via different pleiotropic effects, suggesting that TREM-2 agonism should be investigated as it might beneficially impact HCC pathogenesis in a multifactorial manner.
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Affiliation(s)
- Aitor Esparza-Baquer
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain
| | - Ibone Labiano
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain
| | - Omar Sharif
- Institute for Vascular Biology, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria
- Christian Doppler Laboratory for Arginine Metabolism in Rheumatoid Arthritis and Multiple Sclerosis, Vienna, Austria
| | - Aloña Agirre-Lizaso
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain
| | - Fiona Oakley
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Pedro M Rodrigues
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain
- CIBERehd, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Ekaterina Zhuravleva
- Department of Health and Medical Sciences, Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Colm J O'Rourke
- Department of Health and Medical Sciences, Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Elizabeth Hijona
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain
- CIBERehd, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Raul Jimenez-Agüero
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain
| | - Ioana Riaño
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain
| | - Ana Landa
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain
| | - Adelaida La Casta
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain
| | - Marco Y W Zaki
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Biochemistry Department, Faculty of Pharmacy, Minia University, Minya, Egypt
| | - Patricia Munoz-Garrido
- Department of Health and Medical Sciences, Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Mikel Azkargorta
- CIBERehd, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Proteomics Platform, CIC bioGUNE, ProteoRed-ISCIII, Bizkaia Science and Technology Park, Derio, Spain
| | - Felix Elortza
- CIBERehd, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Proteomics Platform, CIC bioGUNE, ProteoRed-ISCIII, Bizkaia Science and Technology Park, Derio, Spain
| | - Andrea Vogel
- Institute for Vascular Biology, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria
- Christian Doppler Laboratory for Arginine Metabolism in Rheumatoid Arthritis and Multiple Sclerosis, Vienna, Austria
| | - Gernot Schabbauer
- Institute for Vascular Biology, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria
- Christian Doppler Laboratory for Arginine Metabolism in Rheumatoid Arthritis and Multiple Sclerosis, Vienna, Austria
| | - Patricia Aspichueta
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Lejona, Spain
| | - Jesper B Andersen
- Department of Health and Medical Sciences, Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Sylvia Knapp
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Medicine I, Laboratory of Infection Biology, Medical University of Vienna, Vienna, Austria
| | - Derek A Mann
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Luis Bujanda
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain
- CIBERehd, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Department of Medicine, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Lejona, Spain
| | - Jesus Maria Banales
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain
- CIBERehd, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Maria Jesus Perugorria
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain
- CIBERehd, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Department of Medicine, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Lejona, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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Matorras R, Valls R, Azkargorta M, Burgos J, Rabanal A, Elortza F, Mas JM, Sardon T. Proteomics based drug repositioning applied to improve in vitro fertilization implantation: an artificial intelligence model. Syst Biol Reprod Med 2021; 67:281-297. [PMID: 34126818 DOI: 10.1080/19396368.2021.1928792] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Embryo implantation is one of the most inefficient steps in assisted reproduction, so the identifying drugs with a potential clinical application to improve it has a strong interest. This work applies artificial intelligence and systems biology-based mathematical modeling strategies to unveil potential treatments by computationally analyzing and integrating available molecular and clinical data from patients. The mathematical models of embryo implantation computationally generated here simulate the molecular networks underneath this biological process. Once generated, these models were analyzed in order to identify potential repositioned drugs (drugs already used for other indications) able to improve embryo implantation by modulating the molecular pathways involved. Interestingly, the repositioning analysis has identified drugs considering two endpoints: (1) drugs able to modulate the activity of proteins whose role in embryo implantation is already bibliographically acknowledged, and (2) drugs that modulate key proteins in embryo implantation previously predicted through a mechanistic analysis of the mathematical models. This second approach increases the scope open for examination and potential novelty of the repositioning strategy. As a result, a list of 23 drug candidates to improve embryo implantation after IVF was identified by the mathematical models. This list includes many of the compounds already tested for this purpose, which reinforces the predictive capacity of our approach, together with novel repositioned candidates (e.g., Infliximab, Polaprezinc, and Amrinone). In conclusion, the present study exploits existing molecular and clinical information to offer new hypotheses regarding molecular mechanisms in embryo implantation and therapeutic candidates to improve it. This information will be very useful to guide future research.Abbreviations: IVF: in vitro fertilization; EI: Embryo implantation; TPMS: Therapeutic Performance Mapping System; MM: mathematical models; ANN: Artificial Neuronal Networks; TNFα: tumour necrosis factor factor-alpha; HSPs: heat shock proteins; VEGF: vascular endothelial growth factor; PPARA: peroxisome proliferator activated receptor-α PXR: pregnane X receptor; TTR: transthyretin; BED: Biological Effectors Database; MLP: multilayer perceptron.
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Affiliation(s)
- Roberto Matorras
- Department of Obstetrics and Gynecology, University of the Basque Country, Bilbao, Spain.,IVIRMA Bilbao, Bilbao, Spain
| | | | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, Derio, Spain
| | - Jorge Burgos
- Biocruces Bizkaia Health Research Institute. Osakidetza. Cruces University Hospital, University of the Basque Country, Bilbao, Spain
| | - Aintzane Rabanal
- Department of Obstetrics and Gynecology, University of the Basque Country, Bilbao, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, Derio, Spain
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32
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Gonzalez E, Azkargorta M, Garcia-Vallicrosa C, Prieto-Elordui J, Elortza F, Blanco-Sampascual S, Falcon-Perez JM. Could protein content of Urinary Extracellular Vesicles be useful to detect Cirrhosis in Alcoholic Liver Disease? Int J Biol Sci 2021; 17:1864-1877. [PMID: 34131392 PMCID: PMC8193259 DOI: 10.7150/ijbs.59725] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/10/2021] [Indexed: 12/13/2022] Open
Abstract
Alcohol abuse has a high impact on the mortality and morbidity related to a great number of diseases and is responsible for the development of alcoholic liver disease (ALD). It remains challenging to detect and evaluate its severity, which is crucial for prognosis. In this work, we studied if urinary EVs (uEVs) could serve in diagnose and evaluate cirrhosis in ALD. To this purpose, uEVs characterization by cryo-electron microscopy (Cryo-EM), Nanoparticle Tracking Analysis (NTA) and Western blotting (WB) was performed in a cohort of 21 controls and 21 cirrhotic patients. Then, proteomics of uEVs was carried out in a second cohort of 6 controls and 8 patients in order to identify new putative biomarkers for cirrhosis in ALD. Interestingly, uEVs concentration, size and protein composition were altered in cirrhotic patients. From a total of 1304 proteins identified in uEVs, 90 of them were found to be altered in cirrhotic patients. The results suggest that uEVs could be considered as a tool and a supplier of new biomarkers for cirrhosis in ALD, whose application would be especially relevant in chronic patients. Yet, further research is necessary to obtain more relevant result in clinical terms.
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Affiliation(s)
- Esperanza Gonzalez
- Exosomes Laboratory. Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Mikel Azkargorta
- Proteomics Platform. Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Clara Garcia-Vallicrosa
- Exosomes Laboratory. Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | | | - Felix Elortza
- Proteomics Platform. Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | | | - Juan Manuel Falcon-Perez
- Exosomes Laboratory. Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Madrid, Spain
- IKERBASQUE Basque Foundation for Science Bilbao Spain
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33
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Groult H, Carregal-Romero S, Castejón D, Azkargorta M, Miguel-Coello AB, Pulagam KR, Gómez-Vallejo V, Cousin R, Muñoz-Caffarel M, Lawrie CH, Llop J, Piot JM, Elortza F, Maugard T, Ruiz-Cabello J, Fruitier-Arnaudin I. Heparin length in the coating of extremely small iron oxide nanoparticles regulates in vivo theranostic applications. Nanoscale 2021; 13:842-861. [PMID: 33351869 DOI: 10.1039/d0nr06378a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The positive contrast of extremely small iron oxide nanoparticles (ESIONP) in magnetic resonance imaging (MRI) rejuvenates this class of metal nanoparticles (NP).Yet, the current synthesis often lacks the possibility of adjusting the core size (while it is a key element for ESIONP-based MRI contrast behaviour), and also involved multiple complex steps before obtaining a ready-to-use probe for medical applications. In this study, we faced these challenges by applying heparin oligosaccharides (HO) of different lengths as coatings for the preparation of HEP-ESIONP with a one-pot microwave method. We demonstrated that the HO length could control the core size during the synthesis to achieve optimal positive MRI contrast, and that HEP-ESIONP were endowed directly with anticoagulant properties and/or a specific antitumor activity, according to the HO used. Relevantly, positron emission tomography (PET)-based in vivo biodistribution study conducted with 68Ga core-doped HEP-ESIONP analogues revealed significant changes in the probe behaviours, the shortening of HO promoting a shift from hepatic to renal clearance. The different conformations of HO coatings and a thorough in vitro characterisation of the probes' protein coronas provided insight into this crucial impact of HO length on opsonization-mediated immune response and elimination. Overall, we were able to identify a precise HO length to get an ESIONP probe showing prolonged vascular lifetime and moderate accumulation in a tumor xenograft, balanced with a low uptake by non-specific organs and favourable urinary clearance. This probe met all prerequisites for advanced theranostic medical applications with a dual MRI/PET hot spot capability and potential antitumor activity.
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Affiliation(s)
- Hugo Groult
- BCBS team (Biotechnologies et Chimie des Bioressources pour la Santé), LIENSs Laboratory (Littoral environment et Sociétés), UMR CNRS 7266, University of La Rochelle, La Rochelle, France.
| | - Susana Carregal-Romero
- CIC biomaGUNE and Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Gipuzkoa, Spain. and CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - David Castejón
- Unidad de RMN - CAI Bioimagen Complutense, Universidad Complutense de Madrid, Spain
| | - Mikel Azkargorta
- Proteomics Platform CIC bioGUNE, Bizkaia Science and Technology, Derio, Spain
| | - Ana-Beatriz Miguel-Coello
- CIC biomaGUNE and Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Gipuzkoa, Spain.
| | - Krishna Reddy Pulagam
- CIC biomaGUNE and Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Gipuzkoa, Spain.
| | - Vanessa Gómez-Vallejo
- CIC biomaGUNE and Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Gipuzkoa, Spain.
| | - Rémi Cousin
- BCBS team (Biotechnologies et Chimie des Bioressources pour la Santé), LIENSs Laboratory (Littoral environment et Sociétés), UMR CNRS 7266, University of La Rochelle, La Rochelle, France.
| | - María Muñoz-Caffarel
- Molecular Oncology Group, Biodonostia Health Research Institute, San Sebastian, Spain and Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Charles H Lawrie
- Molecular Oncology Group, Biodonostia Health Research Institute, San Sebastian, Spain and Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Jordi Llop
- CIC biomaGUNE and Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Gipuzkoa, Spain. and CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Jean-Marie Piot
- BCBS team (Biotechnologies et Chimie des Bioressources pour la Santé), LIENSs Laboratory (Littoral environment et Sociétés), UMR CNRS 7266, University of La Rochelle, La Rochelle, France.
| | - Felix Elortza
- Proteomics Platform CIC bioGUNE, Bizkaia Science and Technology, Derio, Spain
| | - Thierry Maugard
- BCBS team (Biotechnologies et Chimie des Bioressources pour la Santé), LIENSs Laboratory (Littoral environment et Sociétés), UMR CNRS 7266, University of La Rochelle, La Rochelle, France.
| | - Jesús Ruiz-Cabello
- CIC biomaGUNE and Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Gipuzkoa, Spain. and CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain and Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain and Departamento de Química en Ciencias Farmacéuticas, Universidad Complutense de Madrid, Madrid, Spain
| | - Ingrid Fruitier-Arnaudin
- BCBS team (Biotechnologies et Chimie des Bioressources pour la Santé), LIENSs Laboratory (Littoral environment et Sociétés), UMR CNRS 7266, University of La Rochelle, La Rochelle, France.
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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.
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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
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35
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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.
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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:
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Cerqueira A, Romero-Gavilán F, García-Arnáez I, Martinez-Ramos C, Ozturan S, Iloro I, Azkargorta M, Elortza F, Izquierdo R, Gurruchaga M, Goñi I, Suay J. Bioactive zinc-doped sol-gel coating modulates protein adsorption patterns and in vitro cell responses. Mater Sci Eng C Mater Biol Appl 2020; 121:111839. [PMID: 33579477 DOI: 10.1016/j.msec.2020.111839] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/07/2020] [Accepted: 12/20/2020] [Indexed: 02/06/2023]
Abstract
Zinc is an essential element with an important role in stimulating the osteogenesis and mineralization and suppressing osteoclast differentiation. In this study, new bioactive ZnCl2-doped sol-gel materials were designed to be applied as coatings onto titanium. The biomaterials were physicochemically characterized and the cellular responses evaluated in vitro using MC3T3-E1 osteoblasts and RAW264.7 macrophages. The effect of Zn on the adsorption of human serum proteins onto the material surface was evaluated through nLC-MS/MS. The incorporation of Zn did not affect the crosslinking of the sol-gel network. A controlled Zn2+ release was obtained, reaching values below 10 ppm after 21 days. The materials were no cytotoxic and lead to increased gene expression of ALP, TGF-β, and RUNX2 in the osteoblasts. In macrophages, an increase of IL-1β, TGF-β, and IL-4 gene expression was accompanied by a reduced TNF-α liberation. Proteomic results showed changes in the adsorption patterns of proteins associated with immunological, coagulative, and regenerative functions, in a Zn dose-dependent manner. The variations in protein adsorption might lead to the downregulation of the NF-κB pathway, thus explain the observed biological effects of Zn incorporation into biomaterials. Overall, these coatings demonstrated their potential to promote bone tissue regeneration.
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Affiliation(s)
- A Cerqueira
- Department of Industrial Systems Engineering and Design, Universitat Jaume I, Av. Vicent Sos Baynat s/n, 12071 Castellón de la Plana, Spain
| | - F Romero-Gavilán
- Department of Industrial Systems Engineering and Design, Universitat Jaume I, Av. Vicent Sos Baynat s/n, 12071 Castellón de la Plana, Spain.
| | - I García-Arnáez
- Departament of Science and Technology of Polymers, Universidad del País Vasco, P. M. de Lardizábal, 3, 20018 San Sebastián, Spain
| | - C Martinez-Ramos
- Center for Biomaterials and Tissue Engineering, Universitat Politècnica de Valencia, Camino de Vera, s/n, 46022, Valencia, Spain
| | - S Ozturan
- Department of Periodontology, Faculty of Dentristy, Istanbul Medeniyet University, Istanbul, Turkey
| | - I Iloro
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - M Azkargorta
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - F Elortza
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - R Izquierdo
- Department of Industrial Systems Engineering and Design, Universitat Jaume I, Av. Vicent Sos Baynat s/n, 12071 Castellón de la Plana, Spain
| | - M Gurruchaga
- Departament of Science and Technology of Polymers, Universidad del País Vasco, P. M. de Lardizábal, 3, 20018 San Sebastián, Spain
| | - I Goñi
- Departament of Science and Technology of Polymers, Universidad del País Vasco, P. M. de Lardizábal, 3, 20018 San Sebastián, Spain
| | - J Suay
- Department of Industrial Systems Engineering and Design, Universitat Jaume I, Av. Vicent Sos Baynat s/n, 12071 Castellón de la Plana, Spain
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37
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Lachén-Montes M, Mendizuri N, Ausín K, Pérez-Mediavilla A, Azkargorta M, Iloro I, Elortza F, Kondo H, Ohigashi I, Ferrer I, de la Torre R, Robledo P, Fernández-Irigoyen J, Santamaría E. Smelling the Dark Proteome: Functional Characterization of PITH Domain-Containing Protein 1 (C1orf128) in Olfactory Metabolism. J Proteome Res 2020; 19:4826-4843. [PMID: 33185454 DOI: 10.1021/acs.jproteome.0c00452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Human Proteome Project (HPP) consortium aims to functionally characterize the dark proteome. On the basis of the relevance of olfaction in early neurodegeneration, we have analyzed the dark proteome using data mining in public resources and omics data sets derived from the human olfactory system. Multiple dark proteins localize at synaptic terminals and may be involved in amyloidopathies such as Alzheimer's disease (AD). We have characterized the dark PITH domain-containing protein 1 (PITHD1) in olfactory metabolism using bioinformatics, proteomics, in vitro and in vivo studies, and neuropathology. PITHD1-/- mice exhibit olfactory bulb (OB) proteome changes related to synaptic transmission, cognition, and memory. OB PITHD1 expression increases with age in wild-type (WT) mice and decreases in Tg2576 AD mice at late stages. The analysis across 6 neurological disorders reveals that olfactory tract (OT) PITHD1 is specifically upregulated in human AD. Stimulation of olfactory neuroepithelial (ON) cells with PITHD1 alters the ON phosphoproteome, modifies the proliferation rate, and induces a pro-inflammatory phenotype. This workflow applied by the Spanish C-HPP and Human Brain Proteome Project (HBPP) teams across the ON-OB-OT axis can be adapted as a guidance to decipher functional features of dark proteins. Data are available via ProteomeXchange with identifiers PXD018784 and PXD021634.
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Affiliation(s)
- Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
| | - Naroa Mendizuri
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
| | - Karina Ausín
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
| | - Alberto Pérez-Mediavilla
- IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain.,Neurobiology of Alzheimer's Disease, Department of Biochemistry, Center for Applied Medical Research (CIMA), Neurosciences Division, University of Navarra, 31008 Pamplona, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Ibon Iloro
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Hiroyuki Kondo
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Isidre Ferrer
- Bellvitge Biomedical Research Institute (IDIBELL), 08908 Hospitalet de Llobregat, Spain.,CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, 28029 Madrid, Spain.,Department of Pathology and Experimental Therapeutics, University of Barcelona, 08908 Hospitalet de Llobregat, Spain.,Institute of Neurosciences, University of Barcelona, 08007 Barcelona, Spain
| | - Rafael de la Torre
- Integrative Pharmacology and Systems Neuroscience Research Group, Neurosciences Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain.,Department of Experimental and Health Sciences, Pompeu Fabra University (CEXS-UPF), 08002 Barcelona, Spain.,School of Medicine, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Fisiopatología de la Obesidad y Nutrición (CB06/03), CIBEROBN, 28029 Madrid, Spain
| | - Patricia Robledo
- Integrative Pharmacology and Systems Neuroscience Research Group, Neurosciences Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain.,Department of Experimental and Health Sciences, Pompeu Fabra University (CEXS-UPF), 08002 Barcelona, Spain
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
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Fernández-Ramos D, Lopitz-Otsoa F, Delacruz-Villar L, Bilbao J, Pagano M, Mosca L, Bizkarguenaga M, Serrano-Macia M, Azkargorta M, Iruarrizaga-Lejarreta M, Sot J, Tsvirkun D, van Liempd SM, Goni FM, Alonso C, Martínez-Chantar ML, Elortza F, Hayardeny L, Lu SC, Mato JM. Arachidyl amido cholanoic acid improves liver glucose and lipid homeostasis in nonalcoholic steatohepatitis via AMPK and mTOR regulation. World J Gastroenterol 2020; 26:5101-5117. [PMID: 32982112 PMCID: PMC7495035 DOI: 10.3748/wjg.v26.i34.5101] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/19/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Arachidyl amido cholanoic acid (Aramchol) is a potent downregulator of hepatic stearoyl-CoA desaturase 1 (SCD1) protein expression that reduces liver triglycerides and fibrosis in animal models of steatohepatitis. In a phase IIb clinical trial in patients with nonalcoholic steatohepatitis (NASH), 52 wk of treatment with Aramchol reduced blood levels of glycated hemoglobin A1c, an indicator of glycemic control.
AIM To assess lipid and glucose metabolism in mouse hepatocytes and in a NASH mouse model [induced with a 0.1% methionine and choline deficient diet (0.1MCD)] after treatment with Aramchol.
METHODS Isolated primary mouse hepatocytes were incubated with 20 μmol/L Aramchol or vehicle for 48 h. Subsequently, analyses were performed including Western blot, proteomics by mass spectrometry, and fluxomic analysis with 13C-uniformly labeled glucose. For the in vivo part of the study, male C57BL/6J mice were randomly fed a control or 0.1MCD for 4 wk and received 1 or 5 mg/kg/d Aramchol or vehicle by intragastric gavage for the last 2 wk. Liver metabolomics were assessed using ultra-high-performance liquid chromatography-time of flight-MS for the determination of glucose metabolism-related metabolites.
RESULTS Combination of proteomics and Western blot analyses showed increased AMPK activity while the activity of nutrient sensor mTORC1 was decreased by Aramchol in hepatocytes. This translated into changes in the content of their downstream targets including proteins involved in fatty acid (FA) synthesis and oxidation [P-ACCα/β(S79), SCD1, CPT1A/B, HADHA, and HADHB], oxidative phosphorylation (NDUFA9, NDUFB11, NDUFS1, NDUFV1, ETFDH, and UQCRC2), tricarboxylic acid (TCA) cycle (MDH2, SUCLA2, and SUCLG2), and ribosome (P-p70S6K[T389] and P-S6[S235/S236]). Flux experiments with 13C-uniformely labeled glucose showed that TCA cycle cataplerosis was reduced by Aramchol in hepatocytes, as indicated by the increase in the number of rounds that malate remained in the TCA cycle. Finally, liver metabolomic analysis showed that glucose homeostasis was improved by Aramchol in 0.1MCD fed mice in a dose-dependent manner, showing normalization of glucose, G6P, F6P, UDP-glucose, and Rbl5P/Xyl5P.
CONCLUSION Aramchol exerts its effect on glucose and lipid metabolism in NASH through activation of AMPK and inhibition of mTORC1, which in turn activate FA β-oxidation and oxidative phosphorylation.
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Affiliation(s)
- David Fernández-Ramos
- Precision Medicine and Metabolism Laboratory, Centro de Investigación Cooperativa en Biociencias (CIC bioGUNE), Derio 48160, Bizkaia, Spain
- CIBERehd - Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas, Madrid 28029, Spain
| | - Fernando Lopitz-Otsoa
- Precision Medicine and Metabolism Laboratory, Centro de Investigación Cooperativa en Biociencias (CIC bioGUNE), Derio 48160, Bizkaia, Spain
| | - Laura Delacruz-Villar
- Precision Medicine and Metabolism Laboratory, Centro de Investigación Cooperativa en Biociencias (CIC bioGUNE), Derio 48160, Bizkaia, Spain
| | - Jon Bilbao
- Precision Medicine and Metabolism Laboratory, Centro de Investigación Cooperativa en Biociencias (CIC bioGUNE), Derio 48160, Bizkaia, Spain
| | - Martina Pagano
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples 80138, Italy
| | - Laura Mosca
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples 80138, Italy
| | - Maider Bizkarguenaga
- Precision Medicine and Metabolism Laboratory, Centro de Investigación Cooperativa en Biociencias (CIC bioGUNE), Derio 48160, Bizkaia, Spain
| | - Marina Serrano-Macia
- Liver Disease Laboratory, Centro de Investigación Cooperativa en Biociencias (CIC bioGUNE), Derio 48160, Spain
| | - Mikel Azkargorta
- Proteomics Platform, Centro de Investigación Cooperativa en Biociencias (CIC bioGUNE), Derio 48160, Spain
| | | | - Jesús Sot
- Instituto Biofisika (UPV/EHU, CSIC), Leioa 48940, Spain; Departamento de Bioquímica y Biología Molecular, Universidad del País Vasco, Leioa 48940, Spain
| | - Darya Tsvirkun
- Pre-clinical and Chemistry, Manufacturing and Controls, Galmed Pharmaceuticals, Tel Aviv 6578317, Israel
| | | | - Felix M Goni
- Instituto Biofisika (UPV/EHU, CSIC), Leioa 48940, Spain; Departamento de Bioquímica y Biología Molecular, Universidad del País Vasco, Leioa 48940, Spain
| | | | - María Luz Martínez-Chantar
- CIBERehd - Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas, Madrid 28029, Spain
- Liver Disease Laboratory, Centro de Investigación Cooperativa en Biociencias (CIC bioGUNE), Derio 48160, Spain
| | - Felix Elortza
- Proteomics Platform, Centro de Investigación Cooperativa en Biociencias (CIC bioGUNE), Derio 48160, Spain
| | - Liat Hayardeny
- Pre-clinical and Chemistry, Manufacturing and Controls, Galmed Pharmaceuticals, Tel Aviv 6578317, Israel
| | - Shelly C Lu
- Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - José M Mato
- Precision Medicine and Metabolism Laboratory, Centro de Investigación Cooperativa en Biociencias (CIC bioGUNE), Derio 48160, Bizkaia, Spain
- CIBERehd - Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas, Madrid 28029, Spain
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Santos-Laso A, Izquierdo-Sanchez L, Rodrigues PM, Huang BQ, Azkargorta M, Lapitz A, Munoz-Garrido P, Arbelaiz A, Caballero FJ, Fernandez-Barrena MG, Jimenez-Agüero R, Argemi J, Aragon T, Elortza F, Marzioni M, Drenth JP, LaRusso NF, Bujanda L, Perugorria MJ, Banales JM. Proteostasis disturbances and endoplasmic reticulum stress contribute to polycystic liver disease: New therapeutic targets. Liver Int 2020; 40:1670-1685. [PMID: 32378324 PMCID: PMC7370945 DOI: 10.1111/liv.14485] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 12/17/2019] [Revised: 04/07/2020] [Accepted: 04/16/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND & AIMS Polycystic liver diseases (PLDs) are genetic disorders characterized by progressive development of multiple biliary cysts. Recently, novel PLD-causative genes, encoding for endoplasmic reticulum (ER)-resident proteins involved in protein biogenesis and transport, were identified. We hypothesized that aberrant proteostasis contributes to PLD pathogenesis, representing a potential therapeutic target. METHODS ER stress was analysed at transcriptional (qPCR), proteomic (mass spectrometry), morphological (transmission electron microscopy, TEM) and functional (proteasome activity) levels in different PLD models. The effect of ER stress inhibitors [4-phenylbutyric acid (4-PBA)] and/or activators [tunicamycin (TM)] was tested in polycystic (PCK) rats and cystic cholangiocytes in vitro. RESULTS The expression levels of unfolded protein response (UPR) components were upregulated in liver tissue from PLD patients and PCK rats, as well as in primary cultures of human and rat cystic cholangiocytes, compared to normal controls. Cystic cholangiocytes showed altered proteomic profiles, mainly related to proteostasis (ie synthesis, folding, trafficking and degradation of proteins), marked enlargement of the ER lumen (by TEM) and hyperactivation of the proteasome. Notably, chronic treatment of PCK rats with 4-PBA decreased liver weight, as well as both liver and cystic volumes, of animals under baseline conditions or after TM administration compared to controls. In vitro, 4-PBA downregulated the expression (mRNA) of UPR effectors, normalized proteomic profiles related to protein synthesis, folding, trafficking and degradation and reduced the proteasome hyperactivity in cystic cholangiocytes, reducing their hyperproliferation and apoptosis. CONCLUSIONS Restoration of proteostasis in cystic cholangiocytes with 4-PBA halts hepatic cystogenesis, emerging as a novel therapeutic strategy.
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Affiliation(s)
- Alvaro Santos-Laso
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute – Donostia University Hospital –, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Laura Izquierdo-Sanchez
- 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), Madrid, Spain
| | - Pedro M. Rodrigues
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute – Donostia University Hospital –, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Bing Q. Huang
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Mikel Azkargorta
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), Madrid, Spain;,Proteomics Platform, CIC bioGUNE, ProteoRed-ISCIII, Bizkaia Science and Technology Park, Derio, Spain
| | - Ainhoa Lapitz
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute – Donostia University Hospital –, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Patricia Munoz-Garrido
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute – Donostia University Hospital –, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Ander Arbelaiz
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute – Donostia University Hospital –, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Francisco J. Caballero
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute – Donostia University Hospital –, University of the Basque Country (UPV/EHU), San Sebastian, Spain;,Department of Organic Chemistry I, Center for Innovation in Advanced Chemistry (ORFEO-CINQA), University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Maite G. Fernandez-Barrena
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), Madrid, Spain;,Division of Hepatology, CIMA-University of Navarra, Pamplona, Spain
| | - Raul Jimenez-Agüero
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute – Donostia University Hospital –, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | | | - Tomas Aragon
- Division of Hepatology, CIMA-University of Navarra, Pamplona, Spain
| | - Felix Elortza
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), Madrid, Spain;,Proteomics Platform, CIC bioGUNE, ProteoRed-ISCIII, Bizkaia Science and Technology Park, Derio, Spain
| | - Marco Marzioni
- Department of Gastroenterology and Hepatology, Università Politecnica delle Marche, Ancona, Italy
| | - Joost P.H. Drenth
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nicholas F. LaRusso
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Luis 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), Madrid, Spain
| | - Maria J. 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), Madrid, Spain;,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Jesus M. 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), Madrid, Spain;,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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Bozal-Basterra L, Gonzalez-Santamarta M, Muratore V, Bermejo-Arteagabeitia A, Da Fonseca C, Barroso-Gomila O, Azkargorta M, Iloro I, Pampliega O, Andrade R, Martín-Martín N, Branon TC, Ting AY, Rodríguez JA, Carracedo A, Elortza F, Sutherland JD, Barrio R. LUZP1, a novel regulator of primary cilia and the actin cytoskeleton, is a contributing factor in Townes-Brocks Syndrome. eLife 2020; 9:e55957. [PMID: 32553112 PMCID: PMC7363444 DOI: 10.7554/elife.55957] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/18/2020] [Indexed: 12/20/2022] Open
Abstract
Primary cilia are sensory organelles crucial for cell signaling during development and organ homeostasis. Cilia arise from centrosomes and their formation and function is governed by numerous factors. Through our studies on Townes-Brocks Syndrome (TBS), a rare disease linked to abnormal cilia formation in human fibroblasts, we uncovered the leucine-zipper protein LUZP1 as an interactor of truncated SALL1, a dominantly-acting protein causing the disease. Using TurboID proximity labeling and pulldowns, we show that LUZP1 associates with factors linked to centrosome and actin filaments. Here, we show that LUZP1 is a cilia regulator. It localizes around the centrioles and to actin cytoskeleton. Loss of LUZP1 reduces F-actin levels, facilitates ciliogenesis and alters Sonic Hedgehog signaling, pointing to a key role in cytoskeleton-cilia interdependency. Truncated SALL1 increases the ubiquitin proteasome-mediated degradation of LUZP1. Together with other factors, alterations in LUZP1 may be contributing to TBS etiology.
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Affiliation(s)
- Laura Bozal-Basterra
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
| | - María Gonzalez-Santamarta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
| | - Veronica Muratore
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
| | - Aitor Bermejo-Arteagabeitia
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
| | - Carolina Da Fonseca
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
| | - Orhi Barroso-Gomila
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
| | - Mikel Azkargorta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
- CIBERehd, Instituto de Salud Carlos IIIMadridSpain
- ProteoRed-ISCIII, Instituto de Salud Carlos IIIMadridSpain
| | - Ibon Iloro
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
- CIBERehd, Instituto de Salud Carlos IIIMadridSpain
- ProteoRed-ISCIII, Instituto de Salud Carlos IIIMadridSpain
| | - Olatz Pampliega
- Department of Neurosciences, University of the Basque Country, Achucarro Basque Center for Neuroscience-UPV/EHULeioaSpain
| | - Ricardo Andrade
- Analytical & High Resolution Biomedical Microscopy Core Facility, University of the Basque Country (UPV/EHU)LeioaSpain
| | - Natalia Martín-Martín
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
| | - Tess C Branon
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
- Departments of Genetics, Chemistry and Biology, Stanford UniversityStanfordUnited States
| | - Alice Y Ting
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
- Departments of Genetics, Chemistry and Biology, Stanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Jose A Rodríguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU)LeioaSpain
| | - Arkaitz Carracedo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
- CIBERONC, Instituto de Salud Carlos IIIMadridSpain
- Ikerbasque, Basque Foundation for ScienceBilbaoSpain
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU)BilbaoSpain
| | - Felix Elortza
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
- CIBERehd, Instituto de Salud Carlos IIIMadridSpain
- ProteoRed-ISCIII, Instituto de Salud Carlos IIIMadridSpain
| | - James D Sutherland
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology ParkDerioSpain
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Azkargorta M, Bregón-Villahoz M, Escobes I, Ibáñez-Pérez J, Iloro I, Iglesias M, Diez-Zapirain M, Rabanal A, Prieto B, Moragues MD, Matorras R, Elortza F. In-depth proteomics and natural peptidomics analyses reveal antibacterial peptides in human endometrial fluid. J Proteomics 2020; 216:103652. [DOI: 10.1016/j.jprot.2020.103652] [Citation(s) in RCA: 11] [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: 07/30/2019] [Revised: 12/19/2019] [Accepted: 01/16/2020] [Indexed: 12/23/2022]
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Matorras R, Martinez-Arranz I, Arretxe E, Iruarrizaga-Lejarreta M, Corral B, Ibañez-Perez J, Exposito A, Prieto B, Elortza F, Alonso C. The lipidome of endometrial fluid differs between implantative and non-implantative IVF cycles. J Assist Reprod Genet 2019; 37:385-394. [PMID: 31865491 DOI: 10.1007/s10815-019-01670-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/13/2019] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVE To characterize the most relevant changes in the lipidome of endometrial fluid aspirate (EFA) in non-implantative cycles. DESIGN Lipidomics in a prospective cohort study. SETTINGS Reproductive unit of a university hospital. PATIENTS Twenty-nine women undergoing an IVF cycle. Fifteen achieved pregnancy and 14 did not. INTERVENTION Endometrial fluid aspiration immediately before performing embryo transfer. MAIN OUTCOME MEASURES Clinical pregnancy rate and lipidomic profiles obtained on an ultra-high performance liquid chromatography coupled to time-of-flight mass spectrometry (UHPLC-ToF-MS)-based analytical platform. RESULTS The comparative analysis of the lipidomic patterns of endometrial fluid in implantative and non-implantative IVF cycles revealed eight altered metabolites: seven glycerophospholipids and an omega-6 polyunsaturated fatty acid. Then, women with a non-implantative cycle were accurately classified with a support vector machine algorithm including these eight lipid metabolites. The diagnostic performances of the algorithm showed an area under the receiver operating characteristic curve, sensitivity, specificity, and accuracy of 0.893 ± 0.07, 85.7%, 80.0%, and 82.8%, respectively. CONCLUSION A predictive lipidomic signature linked to the implantative status of the endometrial fluid has been found.
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Affiliation(s)
- Roberto Matorras
- Human Reproduction Unit, Cruces University Hospital, BioCruces, University of the Basque Country, Bilbao, Spain. .,Instituto Valenciano de Infertilidad, IVI, Bilbao, Spain.
| | | | - Enara Arretxe
- OWL Metabolomics, Parque Tecnológico de Bizkaia, Derio, Spain
| | | | - Blanca Corral
- Human Reproduction Unit, Cruces University Hospital, BioCruces, University of the Basque Country, Bilbao, Spain
| | - Jone Ibañez-Perez
- Human Reproduction Unit, Cruces University Hospital, BioCruces, University of the Basque Country, Bilbao, Spain
| | - Antonia Exposito
- Human Reproduction Unit, Cruces University Hospital, BioCruces, University of the Basque Country, Bilbao, Spain
| | - Begoña Prieto
- Human Reproduction Unit, Cruces University Hospital, BioCruces, University of the Basque Country, Bilbao, Spain.,Instituto Valenciano de Infertilidad, IVI, Bilbao, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Parque Tecnológico de Bizkaia, Derio, Spain
| | - Cristina Alonso
- OWL Metabolomics, Parque Tecnológico de Bizkaia, Derio, Spain
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Henriques AFA, Matos P, Carvalho AS, Azkargorta M, Elortza F, Matthiesen R, Jordan P. WNK1 phosphorylation sites in TBC1D1 and TBC1D4 modulate cell surface expression of GLUT1. Arch Biochem Biophys 2019; 679:108223. [PMID: 31816312 DOI: 10.1016/j.abb.2019.108223] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/13/2019] [Accepted: 12/05/2019] [Indexed: 02/06/2023]
Abstract
Glucose uptake by mammalian cells is a key mechanism to maintain cell and tissue homeostasis and relies mostly on plasma membrane-localized glucose transporter proteins (GLUTs). Two main cellular mechanisms regulate GLUT proteins in the cell: first, expression of GLUT genes is under dynamic transcriptional control and is used by cancer cells to increase glucose availability. Second, GLUT proteins are regulated by membrane traffic from storage vesicles to the plasma membrane (PM). This latter process is triggered by signaling mechanisms and well-studied in the case of insulin-responsive cells, which activate protein kinase AKT to phosphorylate TBC1D4, a RAB-GTPase activating protein involved in membrane traffic regulation. Previously, we identified protein kinase WNK1 as another kinase able to phosphorylate TBC1D4 and regulate the surface expression of the constitutive glucose transporter GLUT1. Here we describe that downregulation of WNK1 through RNA interference in HEK293 cells led to a 2-fold decrease in PM GLUT1 expression, concomitant with a 60% decrease in glucose uptake. By mass spectrometry, we identified serine (S) 704 in TBC1D4 as a WNK1-regulated phosphorylation site, and also S565 in the paralogue TBC1D1. Transfection of the respective phosphomimetic or unphosphorylatable TBC1D mutants into cells revealed that both affected the cell surface abundance of GLUT1. The results reinforce a regulatory role for WNK1 in cell metabolism and have potential impact for the understanding of cancer cell metabolism and therapeutic options in type 2 diabetes.
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Affiliation(s)
- Andreia F A Henriques
- Department of Human Genetics, National Health Institute 'Dr. Ricardo Jorge', Lisbon, Portugal; BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Paulo Matos
- Department of Human Genetics, National Health Institute 'Dr. Ricardo Jorge', Lisbon, Portugal; BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Ana Sofia Carvalho
- CEDOC-Chronic Diseases Research Centre, Nova Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Mikel Azkargorta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Building 800, Science and Technology Park of Bizkaia, 48160, Derio, Spain
| | - Felix Elortza
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Building 800, Science and Technology Park of Bizkaia, 48160, Derio, Spain
| | - Rune Matthiesen
- CEDOC-Chronic Diseases Research Centre, Nova Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Peter Jordan
- Department of Human Genetics, National Health Institute 'Dr. Ricardo Jorge', Lisbon, Portugal; BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal.
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44
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Lopitz-Otsoa F, Delgado TC, Lachiondo-Ortega S, Azkargorta M, Elortza F, Rodríguez MS, Martínez-Chantar ML. SUMO-Binding Entities (SUBEs) as Tools for the Enrichment, Isolation, Identification, and Characterization of the SUMO Proteome in Liver Cancer. J Vis Exp 2019. [PMID: 31736480 DOI: 10.3791/60098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Post-translational modification is a key mechanism regulating protein homeostasis and function in eukaryotic cells. Among all ubiquitin-like proteins in liver cancer, the modification by SUMO (Small Ubiquitin MOdifier) has been given the most attention. Isolation of endogenous SUMOylated proteins in vivo is challenging due to the presence of active SUMO-specific proteases. Initial studies of SUMOylation in vivo were based on the molecular detection of specific SUMOylated proteins (e.g., by western blot). However, in many cases, antibodies, generally made with non-modified recombinant protein, did not immunoprecipitate SUMOylated forms of the protein of interest. Nickel chromatography has been the other approach to study SUMOylation by capturing histidine-tagged versions of SUMO molecules. This approach is mainly used in cells stably expressing or transiently transfected with His-SUMO molecules. To overcome these limitations, SUMO-binding entities (SUBEs) were developed to isolate endogenous SUMOylated proteins. Herein, we describe all the steps required for the enrichment, isolation, and identification of SUMOylated substrates from human hepatoma cells and hepatic tissues from a liver cancer mouse model by using SUBEs. Firstly, we describe methods involved in the preparation and lysis of the human hepatoma cells and liver tumor tissue samples. Then, a thorough explanation of the preparation of SUBEs and controls is detailed along with the protocol for the protein pull-down assays. Finally, some examples are provided regarding the options available for the identification and characterization of the SUMOylated proteome, namely the use of western-blot analysis for the detection of a specific SUMOylated substrate from liver tumors or the use of proteomics by mass spectrometry for high-throughput characterization of the SUMOylated proteome and interactome in hepatoma cells.
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Affiliation(s)
- Fernando Lopitz-Otsoa
- Liver Disease and Liver Metabolism Lab, CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)
| | - Teresa C Delgado
- Liver Disease and Liver Metabolism Lab, CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)
| | - Sofía Lachiondo-Ortega
- Liver Disease and Liver Metabolism Lab, CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)
| | | | - Felix Elortza
- Proteomics Platforms, CIC bioGUNE, ProteoRED-ISCIII, CIBERehd
| | - Manuel S Rodríguez
- Advanced Technology Institute in Life Sciences (ITAV)-CNRS-IPBS, UbiCARE
| | - María Luz Martínez-Chantar
- Liver Disease and Liver Metabolism Lab, CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd);
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45
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Ugidos N, Mena J, Baquero S, Alloza I, Azkargorta M, Elortza F, Vandenbroeck K. Interactome of the Autoimmune Risk Protein ANKRD55. Front Immunol 2019; 10:2067. [PMID: 31620119 PMCID: PMC6759997 DOI: 10.3389/fimmu.2019.02067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/15/2019] [Indexed: 01/03/2023] Open
Abstract
The ankyrin repeat domain-55 (ANKRD55) gene contains intronic single nucleotide polymorphisms (SNPs) associated with risk to contract multiple sclerosis, rheumatoid arthritis or other autoimmune disorders. Risk alleles of these SNPs are associated with higher levels of ANKRD55 in CD4+ T cells. The biological function of ANKRD55 is unknown, but given that ankyrin repeat domains constitute one of the most common protein-protein interaction platforms in nature, it is likely to function in complex with other proteins. Thus, identification of its protein interactomes may provide clues. We identified ANKRD55 interactomes via recombinant overexpression in HEK293 or HeLa cells and mass spectrometry. One hundred forty-eight specifically interacting proteins were found in total protein extracts and 22 in extracts of sucrose gradient-purified nuclei. Bioinformatic analysis suggested that the ANKRD55-protein partners from total protein extracts were related to nucleotide and ATP binding, enriched in nuclear transport terms and associated with cell cycle and RNA, lipid and amino acid metabolism. The enrichment analysis of the ANKRD55-protein partners from nuclear extracts is related to sumoylation, RNA binding, processes associated with cell cycle, RNA transport, nucleotide and ATP binding. The interaction between overexpressed ANKRD55 isoform 001 and endogenous RPS3, the cohesins SMC1A and SMC3, CLTC, PRKDC, VIM, β-tubulin isoforms, and 14-3-3 isoforms were validated by western blot, reverse immunoprecipitaton and/or confocal microscopy. We also identified three phosphorylation sites in ANKRD55, with S436 exhibiting the highest score as likely 14-3-3 binding phosphosite. Our study suggests that ANKRD55 may exert function(s) in the formation or architecture of multiple protein complexes, and is regulated by (de)phosphorylation reactions. Based on interactome and subcellular localization analysis, ANKRD55 is likely transported into the nucleus by the classical nuclear import pathway and is involved in mitosis, probably via effects associated with mitotic spindle dynamics.
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Affiliation(s)
- Nerea Ugidos
- Neurogenomiks Group, Department of Neuroscience, University of the Basque Country (UPV/EHU), Leioa, Spain.,Achucarro Basque Center for Neuroscience, Leioa, Spain
| | - Jorge Mena
- Neurogenomiks Group, Department of Neuroscience, University of the Basque Country (UPV/EHU), Leioa, Spain.,Achucarro Basque Center for Neuroscience, Leioa, Spain
| | - Sara Baquero
- Neurogenomiks Group, Department of Neuroscience, University of the Basque Country (UPV/EHU), Leioa, Spain.,Achucarro Basque Center for Neuroscience, Leioa, Spain
| | - Iraide Alloza
- Neurogenomiks Group, Department of Neuroscience, University of the Basque Country (UPV/EHU), Leioa, Spain.,Achucarro Basque Center for Neuroscience, Leioa, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Derio, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Derio, Spain
| | - Koen Vandenbroeck
- Neurogenomiks Group, Department of Neuroscience, University of the Basque Country (UPV/EHU), Leioa, Spain.,Achucarro Basque Center for Neuroscience, Leioa, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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46
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Araújo-Gomes N, Romero-Gavilán F, Zhang Y, Martinez-Ramos C, Elortza F, Azkargorta M, Martín de Llano J, Gurruchaga M, Goñi I, van den Beucken J, Suay J. Complement proteins regulating macrophage polarisation on biomaterials. Colloids Surf B Biointerfaces 2019; 181:125-133. [DOI: 10.1016/j.colsurfb.2019.05.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 05/06/2019] [Accepted: 05/16/2019] [Indexed: 01/06/2023]
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47
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Palacios A, Sampedro L, Sevilla IA, Molina E, Gil D, Azkargorta M, Elortza F, Garrido JM, Anguita J, Prados-Rosales R. Mycobacterium tuberculosis extracellular vesicle-associated lipoprotein LpqH as a potential biomarker to distinguish paratuberculosis infection or vaccination from tuberculosis infection. BMC Vet Res 2019; 15:188. [PMID: 31174546 PMCID: PMC6555097 DOI: 10.1186/s12917-019-1941-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 05/30/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Both bovine tuberculosis (TB) and paratuberculosis (PTB) are serious and widespread bacterial infections affecting many domestic and wild animal species. However, current vaccines do not confer complete protection and cause interference with other diagnostics tests, including bovine TB. Therefore, the development of "Differentiating Infected from Vaccinated Animals" (DIVA) tests are a pressing need. In this study, we have tested the feasibility of mycobacterial extracellular vesicles (EVs) as potential source of biomarkers to discriminate between Mycobacterium bovis infected, Mycobacterium avium subsp. paratuberculosis (MAP) infected and MAP-vaccinated cows. We have, initially, characterized vesicle production in the two most medically relevant species of mycobacteria for livestock, MAP and M. bovis, for being responsible for tuberculosis (TB) and paratuberculosis (PTB). RESULTS Our results indicate that these two species produce EVs with different kinetics, morphology and size distribution. Analysis of the immunogenicity of both type of EVs showed some cross reactivity with sera from PTB+ and TB+ cows, suggesting a limited diagnostic capacity for both EVs. Conversely, we noticed that Mycobacterium tuberculosis (Mtb) EVs showed some differential reactivity between sera from MAP-vaccinated or PTB+ cows from TB+ ones. Mass spectrometry analysis (MS) identified a 19-kDa EV-associated lipoprotein as the main source of the differential reactivity. CONCLUSIONS LpqH could be a good plasma biomarker with capacity to distinguish PTB+ or MAP-vaccinated cows from cows infected with TB.
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Affiliation(s)
- Ainhoa Palacios
- CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48160 Derio, Bizkaia Spain
| | - Leticia Sampedro
- CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48160 Derio, Bizkaia Spain
| | - Iker A. Sevilla
- NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Animal Health Department, Bizkaia Science and Technology Park, Derio, Bizkaia Spain
| | - Elena Molina
- NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Animal Health Department, Bizkaia Science and Technology Park, Derio, Bizkaia Spain
| | - David Gil
- Electron microscopy platform, CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia Spain
| | - Mikel Azkargorta
- Proteomics platform, CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia Spain
| | - Felix Elortza
- Proteomics platform, CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia Spain
| | - Joseba M. Garrido
- NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Animal Health Department, Bizkaia Science and Technology Park, Derio, Bizkaia Spain
| | - Juan Anguita
- CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48160 Derio, Bizkaia Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia Spain
| | - Rafael Prados-Rosales
- CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48160 Derio, Bizkaia Spain
- Department Microbiology and Immunology, Albert Einstein College of Medicine, NY, Bronx, USA
- Department of Preventive Medicine, Public Health and Microbiology, Faculty of Medicine, Autonoma University of Madrid, Madrid, Spain
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48
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Romero-Gavilán F, Araújo-Gomes N, Cerqueira A, García-Arnáez I, Martínez-Ramos C, Azkargorta M, Iloro I, Elortza F, Gurruchaga M, Suay J, Goñi I. Proteomic analysis of calcium-enriched sol-gel biomaterials. J Biol Inorg Chem 2019; 24:563-574. [PMID: 31030324 DOI: 10.1007/s00775-019-01662-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 02/20/2019] [Accepted: 04/15/2019] [Indexed: 01/05/2023]
Abstract
Calcium is an element widely used in the development of biomaterials for bone tissue engineering as it plays important roles in bone metabolism and blood coagulation. The Ca ions can condition the microenvironment at the tissue-material interface, affecting the protein deposition process and cell responses. The aim of this study was to analyze the changes in the patterns of protein adsorption on the silica hybrid biomaterials supplemented with different amounts of CaCl2, which can function as release vehicles. This characterization was carried out by incubating the Ca-biomaterials with human serum. LC-MS/MS analysis was used to characterize the adsorbed protein layers and compile a list of proteins whose affinity for the surfaces might depend on the CaCl2 content. The attachment of pro- and anti-clotting proteins, such as THRB, ANT3, and PROC, increased significantly on the Ca-materials. Similarly, VTNC and APOE, proteins directly involved on osteogenic processes, attached preferentially to these surfaces. To assess correlations with the proteomic data, these formulations were tested in vitro regarding their osteogenic and inflammatory potential, employing MC3T3-E1 and RAW 264.7 cell lines, respectively. The results confirmed a Ca dose-dependent osteogenic and inflammatory behavior of the materials employed, in accordance with the protein attachment patterns.
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Affiliation(s)
- F Romero-Gavilán
- Departamento de Ingeniería de Sistemas Industriales y Diseño, Universitat Jaume I, Av. Vicent-Sos Baynat s/n, 12071, Castellón de la Plana, Spain
| | - Nuno Araújo-Gomes
- Departamento de Ingeniería de Sistemas Industriales y Diseño, Universitat Jaume I, Av. Vicent-Sos Baynat s/n, 12071, Castellón de la Plana, Spain.
- Department of Medicine, Universitat Jaume I, Av. Vicent-Sos Baynat s/n, 12071, Castellón de la Plana, Spain.
| | - A Cerqueira
- Department of Medicine, Universitat Jaume I, Av. Vicent-Sos Baynat s/n, 12071, Castellón de la Plana, Spain
| | - I García-Arnáez
- Facultad de Ciencias Químicas, Universidad del País Vasco., P. M. de Lardizábal, 3, 20018, San Sebastián, Spain
| | - C Martínez-Ramos
- Department of Medicine, Universitat Jaume I, Av. Vicent-Sos Baynat s/n, 12071, Castellón de la Plana, Spain
| | - M Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160, Derio, Spain
| | - I Iloro
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160, Derio, Spain
| | - F Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160, Derio, Spain
| | - M Gurruchaga
- Facultad de Ciencias Químicas, Universidad del País Vasco., P. M. de Lardizábal, 3, 20018, San Sebastián, Spain
| | - J Suay
- Departamento de Ingeniería de Sistemas Industriales y Diseño, Universitat Jaume I, Av. Vicent-Sos Baynat s/n, 12071, Castellón de la Plana, Spain
| | - I Goñi
- Facultad de Ciencias Químicas, Universidad del País Vasco., P. M. de Lardizábal, 3, 20018, San Sebastián, Spain
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49
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Santos-Pérez I, Charro D, Gil-Carton D, Azkargorta M, Elortza F, Bamford DH, Oksanen HM, Abrescia NGA. Structural basis for assembly of vertical single β-barrel viruses. Nat Commun 2019; 10:1184. [PMID: 30862777 PMCID: PMC6414509 DOI: 10.1038/s41467-019-08927-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 09/07/2018] [Accepted: 02/08/2019] [Indexed: 11/10/2022] Open
Abstract
The vertical double β-barrel major capsid protein (MCP) fold, fingerprint of the PRD1-adeno viral lineage, is widespread in many viruses infecting organisms across the three domains of life. The discovery of PRD1-like viruses with two MCPs challenged the known assembly principles. Here, we present the cryo-electron microscopy (cryo-EM) structures of the archaeal, halophilic, internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) and Haloarcula hispanica icosahedral virus 2 (HHIV-2) at 3.7 and 3.8 Å resolution, respectively. Our structures reveal proteins located beneath the morphologically distinct two- and three-tower capsomers and homopentameric membrane proteins at the vertices that orchestrate the positioning of pre-formed vertical single β-barrel MCP heterodimers. The cryo-EM based structures together with the proteomics data provide insights into the assembly mechanism of this type of viruses and into those with membrane-less double β-barrel MCPs. Here, the authors present the cryo-EM structures of two archaeal, halophilic, internal membrane-containing icosahedral viruses at 3.7 and 3.8 Å resolution, providing insights into the assembly process of these and related PRD1-adeno lineage viruses.
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Affiliation(s)
- Isaac Santos-Pérez
- Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160, Derio, Spain
| | - Diego Charro
- Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160, Derio, Spain
| | - David Gil-Carton
- Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160, Derio, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Technology Park, 48160, Derio, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Technology Park, 48160, Derio, Spain
| | - Dennis H Bamford
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 9, 00014, Helsinki, Finland
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 9, 00014, Helsinki, Finland
| | - Nicola G A Abrescia
- Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160, Derio, Spain. .,IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain.
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50
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Romero-Gavilán F, Araújo-Gomes N, García-Arnáez I, Martínez-Ramos C, Elortza F, Azkargorta M, Iloro I, Gurruchaga M, Suay J, Goñi I. The effect of strontium incorporation into sol-gel biomaterials on their protein adsorption and cell interactions. Colloids Surf B Biointerfaces 2018; 174:9-16. [PMID: 30408675 DOI: 10.1016/j.colsurfb.2018.10.075] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 10/11/2018] [Accepted: 10/25/2018] [Indexed: 01/06/2023]
Abstract
It is known strontium can both inhibit the osteoclast formation and stimulate the osteoblast maturation, so biomaterials containing this element can favour bone structure stabilisation. The addition of Sr to biomaterials could affect their interactions with proteins and cells. Here, a silica-hybrid sol-gel network doped with different amounts of SrCl2 and applied as coatings on titanium discs was examined. in vitro analysis was performed to determine the potential effect of Sr in the coatings, showing enhanced gene expression of osteogenic markers (alkaline phosphatase and transforming growth factor-β) in MC3T3-E1 incubated with Sr-doped biomaterials. The examination of inflammatory markers (tumour necrosis factor-α and interleukin 10) in RAW 264.7 macrophages revealed an anti-inflammatory potential of these materials. Proteins adsorbed onto the coatings incubated with human serum (3 h at 37 °C) were also analysed; mass spectrometry was used to characterise the proteins adhering to materials with different Sr content. Adding Sr to the coatings increased their affinity to APOE and VTNC proteins (associated with anti-inflammatory and osteogenic functions). Moreover, the proteins involved in coagulation processes, such as prothrombin, were more abundant on the coatings containing Sr than on the base sol-gel surfaces. Correlations between gene expression and proteomic results were also examined.
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Affiliation(s)
- F Romero-Gavilán
- Departamento de Ingeniería de Sistemas Industriales y Diseño, Universitat Jaume I, Av. Vicent-Sos Baynat s/n. Castellón 12071. Spain
| | - N Araújo-Gomes
- Departamento de Ingeniería de Sistemas Industriales y Diseño, Universitat Jaume I, Av. Vicent-Sos Baynat s/n. Castellón 12071. Spain; Department of Medicine. Universitat Jaume I, Av. Vicent-Sos Baynat s/n. Castellón 12071. Spain.
| | - I García-Arnáez
- Facultad de Ciencias Químicas. Universidad del País Vasco (UPV/EHU). P. M. de Lardizábal, 3. San Sebastián 20018. Spain
| | - C Martínez-Ramos
- Department of Medicine. Universitat Jaume I, Av. Vicent-Sos Baynat s/n. Castellón 12071. Spain
| | - F Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - M Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - I Iloro
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - M Gurruchaga
- Facultad de Ciencias Químicas. Universidad del País Vasco (UPV/EHU). P. M. de Lardizábal, 3. San Sebastián 20018. Spain
| | - J Suay
- Departamento de Ingeniería de Sistemas Industriales y Diseño, Universitat Jaume I, Av. Vicent-Sos Baynat s/n. Castellón 12071. Spain
| | - I Goñi
- Facultad de Ciencias Químicas. Universidad del País Vasco (UPV/EHU). P. M. de Lardizábal, 3. San Sebastián 20018. Spain
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