1
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Espadas G, Llovera L, Ollivier A, Tuorto F, Novoa EM, Sabidó E. Spectral libraries from nucleobases and deoxyribonucleosides facilitate the identification of ribonucleosides by nano-flow liquid chromatography-tandem mass spectrometry. Rapid Commun Mass Spectrom 2024; 38:e9759. [PMID: 38680121 DOI: 10.1002/rcm.9759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/05/2024] [Accepted: 03/31/2024] [Indexed: 05/01/2024]
Abstract
RATIONALE The study addresses the challenge of identifying RNA post-transcriptional modifications when commercial standards are not available to generate reference spectral libraries. It proposes employing homologous nucleobases and deoxyribonucleosides as alternative reference spectral libraries to aid in identifying modified ribonucleosides and distinguishing them from their positional isomers when the standards are unavailable. METHODS Complete sets of ribonucleoside, deoxyribonucleoside and nucleobase standards were analyzed using high-performance nano-flow liquid chromatography coupled to an Orbitrap Eclipse Tribrid mass spectrometer. Spectral libraries were constructed from homologous nucleobases and deoxyribonucleosides using targeted MS2 and neutral-loss-triggered MS3 methods, and collision energies were optimized. The feasibility of using these libraries for identifying modified ribonucleosides and their positional isomers was assessed through comparison of spectral fragmentation patterns. RESULTS Our analysis reveals that both MS2 and neutral-loss-triggered MS3 methods yielded rich spectra with similar fragmentation patterns across ribonucleosides, deoxyribonucleosides and nucleobases. Moreover, we demonstrate that spectra from nucleobases and deoxyribonucleosides, generated at optimized collision energies, exhibited sufficient similarity to those of modified ribonucleosides to enable their use as reference spectra for accurate identification of positional isomers within ribonucleoside families. CONCLUSIONS The study demonstrates the efficacy of utilizing homologous nucleobases and deoxyribonucleosides as interchangeable reference spectral libraries for identifying modified ribonucleosides and their positional isomers. This approach offers a valuable solution for overcoming limitations posed by the unavailability of commercial standards, enhancing the analysis of RNA post-transcriptional modifications via mass spectrometry.
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Affiliation(s)
- Guadalupe Espadas
- Center for Genomics Regulation, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Laia Llovera
- Center for Genomics Regulation, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Alexane Ollivier
- Center for Genomics Regulation, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Francesca Tuorto
- Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Eva Maria Novoa
- Center for Genomics Regulation, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Eduard Sabidó
- Center for Genomics Regulation, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
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2
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Alves-Vale C, Capela AM, Tavares-Marcos C, Domingues-Silva B, Pereira B, Santos F, Gomes CP, Espadas G, Vitorino R, Sabidó E, Borralho P, Nóbrega-Pereira S, Bernardes de Jesus B. Expression of NORAD correlates with breast cancer aggressiveness and protects breast cancer cells from chemotherapy. Mol Ther Nucleic Acids 2023; 33:910-924. [PMID: 37680988 PMCID: PMC10480464 DOI: 10.1016/j.omtn.2023.08.019] [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] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/16/2023] [Indexed: 09/09/2023]
Abstract
The recently discovered human lncRNA NORAD is induced after DNA damage in a p53-dependent manner. It plays a critical role in the maintenance of genomic stability through interaction with Pumilio proteins, limiting the repression of their target mRNAs. Therefore, NORAD inactivation causes chromosomal instability and aneuploidy, which contributes to the accumulation of genetic abnormalities and tumorigenesis. NORAD has been detected in several types of cancer, including breast cancer, which is the most frequently diagnosed and the second-leading cause of cancer death in women. In the present study, we confirmed upregulated NORAD expression levels in a set of human epithelial breast cancer cell lines (MDA-MB-231, MDA-MB-436, and MDA-MB-468), which belong to the most aggressive subtypes (triple-negative breast cancer). These results are in line with previous data showing that high NORAD expression levels in basal-like tumors were associated with poor prognosis. Here, we demonstrate that NORAD downregulation sensitizes triple-negative breast cancer cells to chemotherapy, through a potential accumulation of genomic aberrations and an impaired capacity to signal DNA damage. These results show that NORAD may represent an unexploited neoadjuvant therapeutic target for chemotherapy-unresponsive breast cancer.
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Affiliation(s)
- Catarina Alves-Vale
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
- Hospital CUF Descobertas, CUF Oncologia, 1998-018 Lisbon, Portugal
| | - Ana Maria Capela
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Carlota Tavares-Marcos
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Beatriz Domingues-Silva
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Bruno Pereira
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP – Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Francisco Santos
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Carla Pereira Gomes
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Guadalupe Espadas
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Rui Vitorino
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Eduard Sabidó
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Paula Borralho
- Hospital CUF Descobertas, CUF Oncologia, 1998-018 Lisbon, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Sandrina Nóbrega-Pereira
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Bruno Bernardes de Jesus
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
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3
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Milenkovic I, Santos Vieira HG, Lucas MC, Ruiz-Orera J, Patone G, Kesteven S, Wu J, Feneley M, Espadas G, Sabidó E, Hübner N, van Heesch S, Völkers M, Novoa EM. Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart. Nucleic Acids Res 2023; 51:5301-5324. [PMID: 36882085 PMCID: PMC10287911 DOI: 10.1093/nar/gkad121] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 11/23/2022] [Revised: 01/31/2023] [Accepted: 02/09/2023] [Indexed: 03/09/2023] Open
Abstract
The existence of naturally occurring ribosome heterogeneity is now a well-acknowledged phenomenon. However, whether this heterogeneity leads to functionally diverse 'specialized ribosomes' is still a controversial topic. Here, we explore the biological function of RPL3L (uL3L), a ribosomal protein (RP) paralogue of RPL3 (uL3) that is exclusively expressed in skeletal muscle and heart tissues, by generating a viable homozygous Rpl3l knockout mouse strain. We identify a rescue mechanism in which, upon RPL3L depletion, RPL3 becomes up-regulated, yielding RPL3-containing ribosomes instead of RPL3L-containing ribosomes that are typically found in cardiomyocytes. Using both ribosome profiling (Ribo-seq) and a novel orthogonal approach consisting of ribosome pulldown coupled to nanopore sequencing (Nano-TRAP), we find that RPL3L modulates neither translational efficiency nor ribosome affinity towards a specific subset of transcripts. In contrast, we show that depletion of RPL3L leads to increased ribosome-mitochondria interactions in cardiomyocytes, which is accompanied by a significant increase in ATP levels, potentially as a result of fine-tuning of mitochondrial activity. Our results demonstrate that the existence of tissue-specific RP paralogues does not necessarily lead to enhanced translation of specific transcripts or modulation of translational output. Instead, we reveal a complex cellular scenario in which RPL3L modulates the expression of RPL3, which in turn affects ribosomal subcellular localization and, ultimately, mitochondrial activity.
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Affiliation(s)
- Ivan Milenkovic
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Helaine Graziele Santos Vieira
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Morghan C Lucas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), D-13125 Berlin, Germany
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), D-13125 Berlin, Germany
| | - Scott Kesteven
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Jianxin Wu
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Michael Feneley
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Guadalupe Espadas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Norbert Hübner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), D-13125 Berlin, Germany
- Charité -Universitätsmedizin, D-10117 Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, D-13347 Berlin, Germany
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | | | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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4
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Andrades E, Toll A, Deza G, Segura S, Gimeno R, Espadas G, Sabidó E, Haro N, Pozo ÓJ, Bódalo M, Torres P, Pujol RM, Hernández-Muñoz I. Loss of dyskerin facilitates the acquisition of metastatic traits by altering the mevalonate pathway. Life Sci Alliance 2023; 6:e202201692. [PMID: 36732018 PMCID: PMC9899484 DOI: 10.26508/lsa.202201692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 02/04/2023] Open
Abstract
The initial dissemination of cancer cells from many primary tumors implies intravasation to lymphatic nodes or blood vessels. To investigate the mechanisms involved, we analyzed the expression of small non-coding RNAs in cutaneous squamous cell carcinoma (cSCC), a prevalent tumor that mainly spreads to lymph nodes. We report the reduced expression of small nucleolar RNAs in primary cSCCs that metastasized when compared to non-metastasizing cSCCs, and the progressive loss of DKC1 (dyskerin, which stabilizes the small nucleolar RNAs) along the metastasis. DKC1 depletion in cSCC cells triggered lipid metabolism by altering the mevalonate pathway and the acquisition of metastatic traits. Treatment of DKC1-depleted cells with simvastatin, an inhibitor of the mevalonate pathway, blocked the expression of proteins involved in the epithelial-to-mesenchymal transition. Consistently, the expression of the enzyme 3-hydroxy-3-methylglutaryl-CoA synthase 1 was associated with pathological features of high metastatic risk in cSCC patients. Our data underpin the relevance of the mevalonate metabolism in metastatic dissemination and pave the possible incorporation of therapeutic approaches among the antineoplastic drugs used in routine patient care.
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Affiliation(s)
- Evelyn Andrades
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Agustí Toll
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Department of Dermatology, Hospital Clínic de Barcelona, University of Barcelona and Institut d'Investigacions Biomèdiques August Pi i Sunyer; Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
| | - Gustavo Deza
- Department of Dermatology, Hospital del Mar, Parc de Salut Mar, Barcelona, Spain
| | - Sonia Segura
- Department of Dermatology, Hospital del Mar, Parc de Salut Mar, Barcelona, Spain
| | - Ramón Gimeno
- Laboratory of Immunology, Department of Pathology, Hospital del Mar, Parc de Salut Mar, Barcelona, Spain
| | - Guadalupe Espadas
- Proteomics Unit, Centre de Regulació Genòmica, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Centre de Regulació Genòmica, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Noemí Haro
- Applied Metabolomics Research Group, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Óscar J Pozo
- Applied Metabolomics Research Group, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Marta Bódalo
- MARGenomics, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Paloma Torres
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Ramon M Pujol
- Department of Dermatology, Hospital del Mar, Parc de Salut Mar, Barcelona, Spain
| | - Inmaculada Hernández-Muñoz
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
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5
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Espadas G, Morales-Sanfrutos J, Medina R, Lucas MC, Novoa EM, Sabidó E. High-performance nano-flow liquid chromatography column combined with high- and low-collision energy data-independent acquisition enables targeted and discovery identification of modified ribonucleotides by mass spectrometry. J Chromatogr A 2022; 1665:462803. [PMID: 35042139 DOI: 10.1016/j.chroma.2022.462803] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/29/2021] [Accepted: 01/01/2022] [Indexed: 01/10/2023]
Abstract
Over 170 post-transcriptional RNA modifications have been described and are common in all kingdoms of life. These modifications range from methylation to complex chemical structures, with methylation being the most abundant. RNA modifications play a key role in RNA folding and function and their dysregulation in humans has been linked to several diseases such as cancer, metabolic diseases or neurological disorder. Nowadays, liquid chromatography-tandem mass spectrometry is considered the gold standard method for the identification and quantification of these modifications due to its sensitivity and accuracy. However, the analysis of modified ribonucleosides by mass spectrometry is complex due to the presence of positional isomers. In this scenario, optimal separation of these compounds by highly sensitive liquid chromatography combined with the generation of high-information spectra is critical to unequivocally identify them, especially in high-complex mixtures. Here we present an analytical method that comprises a new type of mixed-mode nano-flow liquid chromatography column combined with high- and low-collision energy data-independent mass spectrometric acquisition for the identification and quantitation of modified ribonucleosides. The method produces content-rich spectra and combines targeted and screening capabilities thus enabling the identification of a variety of modified nucleosides in biological matrices by single-shot liquid chromatographic analysis coupled to mass spectrometry.
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Affiliation(s)
- Guadalupe Espadas
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain; Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Julia Morales-Sanfrutos
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain; Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Rebeca Medina
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
| | - Morghan C Lucas
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain; Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Eva Maria Novoa
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain; Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Eduard Sabidó
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain; Universitat Pompeu Fabra, 08003, Barcelona, Spain.
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6
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Ribera J, Portolés I, Córdoba-Jover B, Rodríguez-Vita J, Casals G, González-de la Presa B, Graupera M, Solsona-Vilarrasa E, Garcia-Ruiz C, Fernández-Checa JC, Soria G, Tudela R, Esteve-Codina A, Espadas G, Sabidó E, Jiménez W, Sessa WC, Morales-Ruiz M. The loss of DHX15 impairs endothelial energy metabolism, lymphatic drainage and tumor metastasis in mice. Commun Biol 2021; 4:1192. [PMID: 34654883 PMCID: PMC8519955 DOI: 10.1038/s42003-021-02722-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 11/20/2020] [Accepted: 09/24/2021] [Indexed: 01/29/2023] Open
Abstract
DHX15 is a downstream substrate for Akt1, which is involved in key cellular processes affecting vascular biology. Here, we explored the vascular regulatory function of DHX15. Homozygous DHX15 gene deficiency was lethal in mouse and zebrafish embryos. DHX15-/- zebrafish also showed downregulation of VEGF-C and reduced formation of lymphatic structures during development. DHX15+/- mice depicted lower vascular density and impaired lymphatic function postnatally. RNAseq and proteome analysis of DHX15 silenced endothelial cells revealed differential expression of genes involved in the metabolism of ATP biosynthesis. The validation of these results demonstrated a lower activity of the Complex I in the mitochondrial membrane of endothelial cells, resulting in lower intracellular ATP production and lower oxygen consumption. After injection of syngeneic LLC1 tumor cells, DHX15+/- mice showed partially inhibited primary tumor growth and reduced lung metastasis. Our results revealed an important role of DHX15 in vascular physiology and pave a new way to explore its potential use as a therapeutical target for metastasis treatment.
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Affiliation(s)
- Jordi Ribera
- Biochemistry and Molecular Genetics Department, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Irene Portolés
- Biochemistry and Molecular Genetics Department, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Bernat Córdoba-Jover
- Biochemistry and Molecular Genetics Department, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Juan Rodríguez-Vita
- Biochemistry and Molecular Genetics Department, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- German Cancer Research Center, Heidelberg, Germany
| | - Gregori Casals
- Biochemistry and Molecular Genetics Department, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Bernardino González-de la Presa
- Biochemistry and Molecular Genetics Department, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Mariona Graupera
- Vascular Signalling Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL). CIBERonc, Barcelona, Spain
| | - Estel Solsona-Vilarrasa
- 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, 08036, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - Carmen Garcia-Ruiz
- 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, 08036, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, 28029, Spain
- USC Research Center for ALPD, Keck School of Medicine, Los Angeles, CA, 90033, USA
| | - José C Fernández-Checa
- 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, 08036, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, 28029, Spain
- USC Research Center for ALPD, Keck School of Medicine, Los Angeles, CA, 90033, USA
| | - Guadalupe Soria
- Experimental 7T-MRI Unit, IDIBAPS, Barcelona, Spain
- CIBERbbn, University of Barcelona, Barcelona, Spain
| | - Raúl Tudela
- Experimental 7T-MRI Unit, IDIBAPS, Barcelona, Spain
- CIBERbbn, University of Barcelona, Barcelona, Spain
| | - Anna Esteve-Codina
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Guadalupe Espadas
- Proteomics Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra, Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra, Barcelona, Spain
| | - Wladimiro Jiménez
- Biochemistry and Molecular Genetics Department, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- Department of Biomedicine-Biochemistry Unit, School of Medicine University of Barcelona, Barcelona, Spain
| | - William C Sessa
- Department of Pharmacology, Department of Cardiology, Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
| | - Manuel Morales-Ruiz
- Biochemistry and Molecular Genetics Department, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain.
- Department of Biomedicine-Biochemistry Unit, School of Medicine University of Barcelona, Barcelona, Spain.
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7
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Olivella R, Chiva C, Serret M, Mancera D, Cozzuto L, Hermoso A, Borràs E, Espadas G, Morales J, Pastor O, Solé A, Ponomarenko J, Sabidó E. QCloud2: An Improved Cloud-based Quality-Control System for Mass-Spectrometry-based Proteomics Laboratories. J Proteome Res 2021; 20:2010-2013. [PMID: 33724836 DOI: 10.1021/acs.jproteome.0c00853] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
QCloud is a cloud-based system to support proteomics laboratories in daily quality assessment using a user-friendly interface, easy setup, and automated data processing. Since its release, QCloud has facilitated automated quality control for proteomics experiments in many laboratories. QCloud provides a quick and effortless evaluation of instrument performance that helps to overcome many analytical challenges derived from clinical and translational research. Here we present an improved version of the system, QCloud2. This new version includes enhancements in the scalability and reproducibility of the quality-control pipelines, and it features an improved front end for data visualization, user management, and chart annotation. The QCloud2 system also includes programmatic access and a standalone local version.
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Affiliation(s)
- Roger Olivella
- Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Cristina Chiva
- Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Marc Serret
- Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Daniel Mancera
- Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Luca Cozzuto
- Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Antoni Hermoso
- Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Eva Borràs
- Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Guadalupe Espadas
- Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Julia Morales
- Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Olga Pastor
- Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Amanda Solé
- Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Julia Ponomarenko
- Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Eduard Sabidó
- Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Spain
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8
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Harjivan SG, Charneira C, Martins IL, Pereira SA, Espadas G, Sabidó E, Beland FA, Marques MM, Antunes AMM. Covalent Histone Modification by an Electrophilic Derivative of the Anti-HIV Drug Nevirapine. Molecules 2021; 26:1349. [PMID: 33802579 PMCID: PMC7961589 DOI: 10.3390/molecules26051349] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 12/20/2022] Open
Abstract
Nevirapine (NVP), a non-nucleoside reverse transcriptase inhibitor widely used in combined antiretroviral therapy and to prevent mother-to-child transmission of the human immunodeficiency virus type 1, is associated with several adverse side effects. Using 12-mesyloxy-nevirapine, a model electrophile of the reactive metabolites derived from the NVP Phase I metabolite, 12-hydroxy-NVP, we demonstrate that the nucleophilic core and C-terminal residues of histones are targets for covalent adduct formation. We identified multiple NVP-modification sites at lysine (e.g., H2BK47, H4K32), histidine (e.g., H2BH110, H4H76), and serine (e.g., H2BS33) residues of the four histones using a mass spectrometry-based bottom-up proteomic analysis. In particular, H2BK47, H2BH110, H2AH83, and H4H76 were found to be potential hot spots for NVP incorporation. Notably, a remarkable selectivity to the imidazole ring of histidine was observed, with modification by NVP detected in three out of the 11 histidine residues of histones. This suggests that NVP-modified histidine residues of histones are prospective markers of the drug's bioactivation and/or toxicity. Importantly, NVP-derived modifications were identified at sites known to determine chromatin structure (e.g., H4H76) or that can undergo multiple types of post-translational modifications (e.g., H2BK47, H4H76). These results open new insights into the molecular mechanisms of drug-induced adverse reactions.
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Affiliation(s)
- Shrika G. Harjivan
- Centro de Química Estrutural (CQE), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; (S.G.H.); (C.C.); (I.L.M.); (M.M.M.)
| | - Catarina Charneira
- Centro de Química Estrutural (CQE), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; (S.G.H.); (C.C.); (I.L.M.); (M.M.M.)
| | - Inês L. Martins
- Centro de Química Estrutural (CQE), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; (S.G.H.); (C.C.); (I.L.M.); (M.M.M.)
| | - Sofia A. Pereira
- Centro de Estudos de Doenças Crónicas (CEDOC), NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1169-056 Lisbon, Portugal;
| | - Guadalupe Espadas
- Proteomics Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; (G.E.); (E.S.)
- Proteomics Unit, Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; (G.E.); (E.S.)
- Proteomics Unit, Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Frederick A. Beland
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA;
| | - M. Matilde Marques
- Centro de Química Estrutural (CQE), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; (S.G.H.); (C.C.); (I.L.M.); (M.M.M.)
| | - Alexandra M. M. Antunes
- Centro de Química Estrutural (CQE), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; (S.G.H.); (C.C.); (I.L.M.); (M.M.M.)
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9
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Quintana-Gallardo L, Martín-Benito J, Marcilla M, Espadas G, Sabidó E, Valpuesta JM. The cochaperone CHIP marks Hsp70- and Hsp90-bound substrates for degradation through a very flexible mechanism. Sci Rep 2019; 9:5102. [PMID: 30911017 PMCID: PMC6433865 DOI: 10.1038/s41598-019-41060-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 01/22/2019] [Indexed: 11/26/2022] Open
Abstract
Some molecular chaperones are involved not only in assisting the folding of proteins but also, given appropriate conditions, in their degradation. This is the case for Hsp70 and Hsp90 which, in concert with the cochaperone CHIP, direct their bound substrate to degradation through ubiquitination. We generated complexes between the chaperones (Hsp70 or Hsp90), the cochaperone CHIP and, as substrate, a p53 variant containing the GST protein (p53-TMGST). Both ternary complexes (Hsp70:p53-TMGST:CHIP and Hsp90:p53-TMGST:CHIP) ubiquitinated the substrate at a higher efficiency than in the absence of the chaperones. The 3D structures of the two complexes, obtained using a combination of cryoelectron microscopy and crosslinking mass spectrometry, showed the substrate located between the chaperone and the cochaperone, suggesting a ubiquitination mechanism in which the chaperone-bound substrate is presented to CHIP. These complexes are inherently flexible, which is important for the ubiquitination process.
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Affiliation(s)
| | | | - Miguel Marcilla
- Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049, Madrid, Spain
| | - Guadalupe Espadas
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
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10
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Rosas-Salvans M, Cavazza T, Espadas G, Sabido E, Vernos I. Proteomic Profiling of Microtubule Self-organization in M-phase. Mol Cell Proteomics 2018; 17:1991-2004. [PMID: 29970457 DOI: 10.1074/mcp.ra118.000745] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 06/11/2018] [Indexed: 01/08/2023] Open
Abstract
Microtubules (MTs) and associated proteins can self-organize into complex structures such as the bipolar spindle, a process in which RanGTP plays a major role. Addition of RanGTP to M-phase Xenopus egg extracts promotes the nucleation and self-organization of MTs into asters and bipolar-like structures in the absence of centrosomes or chromosomes. We show here that the complex proteome of these RanGTP-induced MT assemblies is similar to that of mitotic spindles. Using proteomic profiling we show that MT self-organization in the M-phase cytoplasm involves the non-linear and non-stoichiometric recruitment of proteins from specific functional groups. Our study provides for the first time a temporal understanding of the protein dynamics driving MT self-organization in M-phase.
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Affiliation(s)
- Miquel Rosas-Salvans
- From the ‡Cell and Developmental Biology Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Tommaso Cavazza
- From the ‡Cell and Developmental Biology Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Guadalupe Espadas
- **Proteomics Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.,§Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Eduard Sabido
- **Proteomics Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.,§Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Isabelle Vernos
- From the ‡Cell and Developmental Biology Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; .,§Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain.,‡‡Institució Catalana de Recerca I Estudis Avançats (ICREA), Passeig de Lluis Companys 23, 08010 Barcelona, Spain
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11
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Chiva C, Olivella R, Borràs E, Espadas G, Pastor O, Solé A, Sabidó E. QCloud: A cloud-based quality control system for mass spectrometry-based proteomics laboratories. PLoS One 2018; 13:e0189209. [PMID: 29324744 PMCID: PMC5764250 DOI: 10.1371/journal.pone.0189209] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 11/21/2017] [Indexed: 01/03/2023] Open
Abstract
The increasing number of biomedical and translational applications in mass spectrometry-based proteomics poses new analytical challenges and raises the need for automated quality control systems. Despite previous efforts to set standard file formats, data processing workflows and key evaluation parameters for quality control, automated quality control systems are not yet widespread among proteomics laboratories, which limits the acquisition of high-quality results, inter-laboratory comparisons and the assessment of variability of instrumental platforms. Here we present QCloud, a cloud-based system to support proteomics laboratories in daily quality assessment using a user-friendly interface, easy setup, automated data processing and archiving, and unbiased instrument evaluation. QCloud supports the most common targeted and untargeted proteomics workflows, it accepts data formats from different vendors and it enables the annotation of acquired data and reporting incidences. A complete version of the QCloud system has successfully been developed and it is now open to the proteomics community (http://qcloud.crg.eu). QCloud system is an open source project, publicly available under a Creative Commons License Attribution-ShareAlike 4.0.
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Affiliation(s)
- Cristina Chiva
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Barcelona
- Universitat Pompeu Fabra (UPF), Barcelona, Barcelona
| | - Roger Olivella
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Barcelona
- Universitat Pompeu Fabra (UPF), Barcelona, Barcelona
| | - Eva Borràs
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Barcelona
- Universitat Pompeu Fabra (UPF), Barcelona, Barcelona
| | - Guadalupe Espadas
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Barcelona
- Universitat Pompeu Fabra (UPF), Barcelona, Barcelona
| | - Olga Pastor
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Barcelona
- Universitat Pompeu Fabra (UPF), Barcelona, Barcelona
| | - Amanda Solé
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Barcelona
- Universitat Pompeu Fabra (UPF), Barcelona, Barcelona
| | - Eduard Sabidó
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Barcelona
- Universitat Pompeu Fabra (UPF), Barcelona, Barcelona
- * E-mail:
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12
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Imperlini E, Gnecchi M, Rognoni P, Sabidò E, Ciuffreda MC, Palladini G, Espadas G, Mancuso FM, Bozzola M, Malpasso G, Valentini V, Palladini G, Orrù S, Ferraro G, Milani P, Perlini S, Salvatore F, Merlini G, Lavatelli F. Proteotoxicity in cardiac amyloidosis: amyloidogenic light chains affect the levels of intracellular proteins in human heart cells. Sci Rep 2017; 7:15661. [PMID: 29142197 PMCID: PMC5688098 DOI: 10.1038/s41598-017-15424-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 10/27/2017] [Indexed: 12/31/2022] Open
Abstract
AL amyloidosis is characterized by widespread deposition of immunoglobulin light chains (LCs) as amyloid fibrils. Cardiac involvement is frequent and leads to life-threatening cardiomyopathy. Besides the tissue alteration caused by fibrils, clinical and experimental evidence indicates that cardiac damage is also caused by proteotoxicity of prefibrillar amyloidogenic species. As in other amyloidoses, the damage mechanisms at cellular level are complex and largely undefined. We have characterized the molecular changes in primary human cardiac fibroblasts (hCFs) exposed in vitro to soluble amyloidogenic cardiotoxic LCs from AL cardiomyopathy patients. To evaluate proteome alterations caused by a representative cardiotropic LC, we combined gel-based with label-free shotgun analysis and performed bioinformatics and data validation studies. To assess the generalizability of our results we explored the effects of multiple LCs on hCF viability and on levels of a subset of cellular proteins. Our results indicate that exposure of hCFs to cardiotropic LCs translates into proteome remodeling, associated with apoptosis activation and oxidative stress. The proteome alterations affect proteins involved in cytoskeletal organization, protein synthesis and quality control, mitochondrial activity and metabolism, signal transduction and molecular trafficking. These results support and expand the concept that soluble amyloidogenic cardiotropic LCs exert toxic effects on cardiac cells.
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Affiliation(s)
- Esther Imperlini
- IRCCS SDN, Naples, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Massimiliano Gnecchi
- Coronary Care Unit and Laboratory of Experimental Cardiology for Cell and Molecular Therapy, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Department of Molecular Medicine, Unit of Cardiology, University of Pavia, Pavia, Italy.,Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Paola Rognoni
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Eduard Sabidò
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Maria Chiara Ciuffreda
- Coronary Care Unit and Laboratory of Experimental Cardiology for Cell and Molecular Therapy, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Giovanni Palladini
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Guadalupe Espadas
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Francesco Mattia Mancuso
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Margherita Bozzola
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Giuseppe Malpasso
- Coronary Care Unit and Laboratory of Experimental Cardiology for Cell and Molecular Therapy, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Veronica Valentini
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Giuseppina Palladini
- Department of Internal Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Stefania Orrù
- IRCCS SDN, Naples, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy.,Department of Movement Sciences, "Parthenope" University, Naples, Italy
| | - Giovanni Ferraro
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Paolo Milani
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Stefano Perlini
- Department of Internal Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
| | - Francesco Salvatore
- CEINGE-Biotecnologie Avanzate, Naples, Italy. .,Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Pavia, Italy.
| | - Giampaolo Merlini
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy.
| | - Francesca Lavatelli
- Amyloidosis Research and Treatment Center, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo and University of Pavia, Pavia, Italy
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13
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Vialas V, Colomé-Calls N, Abian J, Aloria K, Alvarez-Llamas G, Antúnez O, Arizmendi JM, Azkargorta M, Barceló-Batllori S, Barderas MG, Blanco F, Casal JI, Casas V, de la Torre C, Chicano-Gálvez E, Elortza F, Espadas G, Estanyol JM, Fernandez-Irigoyen J, Fernandez-Puente P, Fidalgo MJ, Fuentes M, Gay M, Gil C, Hainard A, Hernaez ML, Ibarrola N, Kopylov AT, Lario A, Lopez JA, López-Lucendo M, Marcilla M, Marina-Ramírez A, Marko-Varga G, Martín L, Mora MI, Morato-López E, Muñoz J, Odena MA, de Oliveira E, Orera I, Ortea I, Pasquarello C, Ray KB, Rezeli M, Ruppen I, Sabidó E, Del Pino MMS, Sancho J, Santamaría E, Vazquez J, Vilaseca M, Vivanco F, Walters JJ, Zgoda VG, Corrales FJ, Canals F, Paradela A. A multicentric study to evaluate the use of relative retention times in targeted proteomics. J Proteomics 2016; 152:138-149. [PMID: 27989941 DOI: 10.1016/j.jprot.2016.10.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/27/2016] [Accepted: 10/24/2016] [Indexed: 12/19/2022]
Abstract
Despite the maturity reached by targeted proteomic strategies, reliable and standardized protocols are urgently needed to enhance reproducibility among different laboratories and analytical platforms, facilitating a more widespread use in biomedical research. To achieve this goal, the use of dimensionless relative retention times (iRT), defined on the basis of peptide standard retention times (RT), has lately emerged as a powerful tool. The robustness, reproducibility and utility of this strategy were examined for the first time in a multicentric setting, involving 28 laboratories that included 24 of the Spanish network of proteomics laboratories (ProteoRed-ISCIII). According to the results obtained in this study, dimensionless retention time values (iRTs) demonstrated to be a useful tool for transferring and sharing peptide retention times across different chromatographic set-ups both intra- and inter-laboratories. iRT values also showed very low variability over long time periods. Furthermore, parallel quantitative analyses showed a high reproducibility despite the variety of experimental strategies used, either MRM (multiple reaction monitoring) or pseudoMRM, and the diversity of analytical platforms employed. BIOLOGICAL SIGNIFICANCE From the very beginning of proteomics as an analytical science there has been a growing interest in developing standardized methods and experimental procedures in order to ensure the highest quality and reproducibility of the results. In this regard, the recent (2012) introduction of the dimensionless retention time concept has been a significant advance. In our multicentric (28 laboratories) study we explore the usefulness of this concept in the context of a targeted proteomics experiment, demonstrating that dimensionless retention time values is a useful tool for transferring and sharing peptide retention times across different chromatographic set-ups.
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Affiliation(s)
- Vital Vialas
- ProteoRed-ISCIII, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Núria Colomé-Calls
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain
| | - Joaquín Abian
- ProteoRed-ISCIII, Instituto de Investigaciones Biomédicas de Barcelona, IIBB-CSIC/IDIBAPS, Barcelona 08036, Spain
| | - Kerman Aloria
- Department of Biochemistry and Molecular Biology, University of the Basque Country-UPV/EHU, Leioa 48940, Spain
| | | | - Oreto Antúnez
- ProteoRed-ISCIII, SCSIE Universitat de Valencia, Burjassot 46100, Spain
| | - Jesus M Arizmendi
- ProteoRed-ISCIII, University of the Basque Country-UPV/EHU, Leioa 48940, Spain
| | - Mikel Azkargorta
- ProteoRed-ISCIII, CIC bioGUNE, Science and Technology Park of Bizkaia, Derio, Spain
| | | | - María G Barderas
- ProteoRed-ISCIII, Hospital Nacional de Parapléjicos-SESCAM, Toledo, Spain
| | | | - J Ignacio Casal
- ProteoRed-ISCIII, Centro de Investigaciones Biológicas-CSIC, Madrid 28040, Spain
| | - Vanessa Casas
- ProteoRed-ISCIII, Instituto de Investigaciones Biomédicas de Barcelona, IIBB-CSIC/IDIBAPS, Barcelona 08036, Spain
| | - Carolina de la Torre
- ProteoRed-ISCIII, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Eduardo Chicano-Gálvez
- ProteoRed-ISCIII, Maimonides Institute for Biomedical Research and Universidad de Córdoba, Córdoba 14004, Spain
| | - Felix Elortza
- ProteoRed-ISCIII, CIC bioGUNE, Science and Technology Park of Bizkaia, Derio, Spain
| | - Guadalupe Espadas
- ProteoRed-ISCIII, Centre de Regulació Genòmica, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Josep M Estanyol
- ProteoRed-ISCIII, Scientific and Technological Centers (CCiTUB), University of Barcelona, Barcelona 08036, Spain
| | | | | | - María José Fidalgo
- ProteoRed-ISCIII, Scientific and Technological Centers (CCiTUB), University of Barcelona, Barcelona 08036, Spain
| | - Manuel Fuentes
- ProteoRed-ISCIII, Cancer Research Center, University of Salamanca-CSIC, IBSAL, Salamanca 37007, Spain
| | - Marina Gay
- ProteoRed-ISCIII, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain
| | - Concha Gil
- ProteoRed-ISCIII, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Alexandre Hainard
- Proteomics Core Facility CMU, University of Geneva, Geneva, Switzerland
| | | | - Nieves Ibarrola
- ProteoRed-ISCIII, Cancer Research Center, University of Salamanca-CSIC, IBSAL, Salamanca 37007, Spain
| | - Arthur T Kopylov
- Orekhovich Institute of Biomedical Chemistry RAMS, Moscow 119121, Russian Federation
| | - Antonio Lario
- ProteoRed-ISCIII, IPBLN (CSIC), Armilla, Granada, Spain
| | - Juan Antonio Lopez
- ProteoRed-ISCIII, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - María López-Lucendo
- ProteoRed-ISCIII, Centro de Investigaciones Biológicas-CSIC, Madrid 28040, Spain
| | - Miguel Marcilla
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), Madrid 28049, Spain
| | | | - Gyorgy Marko-Varga
- Centre of Excellence in Biological and Medical Mass spectrometry, Lund University, Lund, Sweden
| | - Luna Martín
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain
| | - Maria I Mora
- ProteoRed-ISCIII, CIMA, University of Navarra, Pamplona 31008, Spain
| | | | - Javier Muñoz
- ProteoRed-ISCIII, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | | | | | - Irene Orera
- ProteoRed-ISCIII, Instituto Aragonés de Ciencias de la Salud, Zaragoza 50009, Spain
| | - Ignacio Ortea
- ProteoRed-ISCIII, Maimonides Institute for Biomedical Research and Universidad de Córdoba, Córdoba 14004, Spain
| | - Carla Pasquarello
- Proteomics Core Facility CMU, University of Geneva, Geneva, Switzerland
| | | | - Melinda Rezeli
- Centre of Excellence in Biological and Medical Mass spectrometry, Lund University, Lund, Sweden
| | - Isabel Ruppen
- ProteoRed-ISCIII, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Eduard Sabidó
- ProteoRed-ISCIII, Centre de Regulació Genòmica, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | | | - Jaime Sancho
- ProteoRed-ISCIII, IPBLN (CSIC), Armilla, Granada, Spain
| | - Enrique Santamaría
- ProteoRed-ISCIII, Navarrabiomed Biomedical Research Center-IdiSNa, Pamplona, Spain
| | - Jesus Vazquez
- ProteoRed-ISCIII, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Marta Vilaseca
- ProteoRed-ISCIII, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain
| | | | | | - Victor G Zgoda
- Orekhovich Institute of Biomedical Chemistry RAMS, Moscow 119121, Russian Federation
| | | | - Francesc Canals
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain.
| | - Alberto Paradela
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), Madrid 28049, Spain.
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14
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Engelken J, Espadas G, Mancuso FM, Bonet N, Scherr AL, Jímenez-Álvarez V, Codina-Solà M, Medina-Stacey D, Spataro N, Stoneking M, Calafell F, Sabidó E, Bosch E. Signatures of Evolutionary Adaptation in Quantitative Trait Loci Influencing Trace Element Homeostasis in Liver. Mol Biol Evol 2016; 33:738-54. [PMID: 26582562 PMCID: PMC4760079 DOI: 10.1093/molbev/msv267] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Essential trace elements possess vital functions at molecular, cellular, and physiological levels in health and disease, and they are tightly regulated in the human body. In order to assess variability and potential adaptive evolution of trace element homeostasis, we quantified 18 trace elements in 150 liver samples, together with the expression levels of 90 genes and abundances of 40 proteins involved in their homeostasis. Additionally, we genotyped 169 single nucleotide polymorphism (SNPs) in the same sample set. We detected significant associations for 8 protein quantitative trait loci (pQTL), 10 expression quantitative trait loci (eQTLs), and 15 micronutrient quantitative trait loci (nutriQTL). Six of these exceeded the false discovery rate cutoff and were related to essential trace elements: 1) one pQTL for GPX2 (rs10133290); 2) two previously described eQTLs for HFE (rs12346) and SELO (rs4838862) expression; and 3) three nutriQTLs: The pathogenic C282Y mutation at HFE affecting iron (rs1800562), and two SNPs within several clustered metallothionein genes determining selenium concentration (rs1811322 and rs904773). Within the complete set of significant QTLs (which involved 30 SNPs and 20 gene regions), we identified 12 SNPs with extreme patterns of population differentiation (FST values in the top 5% percentile in at least one HapMap population pair) and significant evidence for selective sweeps involving QTLs at GPX1, SELENBP1, GPX3, SLC30A9, and SLC39A8. Overall, this detailed study of various molecular phenotypes illustrates the role of regulatory variants in explaining differences in trace element homeostasis among populations and in the human adaptive response to environmental pressures related to micronutrients.
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Affiliation(s)
- Johannes Engelken
- †These authors contributed equally to this work. ‡Deceased October 23, 2015. Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Guadalupe Espadas
- †These authors contributed equally to this work. Proteomics Unit, Center of Genomics Regulation, Barcelona, Spain Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesco M Mancuso
- Proteomics Unit, Center of Genomics Regulation, Barcelona, Spain Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nuria Bonet
- Genomics Core Facility, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Spain
| | - Anna-Lena Scherr
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Victoria Jímenez-Álvarez
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Marta Codina-Solà
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Daniel Medina-Stacey
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nino Spataro
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Francesc Calafell
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Center of Genomics Regulation, Barcelona, Spain Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Elena Bosch
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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Percy AJ, Tamura-Wells J, Albar JP, Aloria K, Amirkhani A, Araujo GD, Arizmendi JM, Blanco FJ, Canals F, Cho JY, Colomé-Calls N, Corrales FJ, Domont G, Espadas G, Fernandez-Puente P, Gil C, Haynes PA, Hernáez ML, Kim JY, Kopylov A, Marcilla M, McKay MJ, Mirzaei M, Molloy MP, Ohlund LB, Paik YK, Paradela A, Raftery M, Sabidó E, Sleno L, Wilffert D, Wolters JC, Yoo JS, Zgoda V, Parker CE, Borchers CH. Inter-laboratory evaluation of instrument platforms and experimental workflows for quantitative accuracy and reproducibility assessment. EuPA Open Proteomics 2015. [DOI: 10.1016/j.euprot.2015.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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16
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Meijer HJG, Mancuso FM, Espadas G, Seidl MF, Chiva C, Govers F, Sabidó E. Profiling the secretome and extracellular proteome of the potato late blight pathogen Phytophthora infestans. Mol Cell Proteomics 2014; 13:2101-13. [PMID: 24872595 PMCID: PMC4125740 DOI: 10.1074/mcp.m113.035873] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 05/09/2014] [Indexed: 11/06/2022] Open
Abstract
Oomycetes are filamentous organisms that cause notorious diseases, several of which have a high economic impact. Well known is Phytophthora infestans, the causal agent of potato late blight. Previously, in silico analyses of the genome and transcriptome of P. infestans resulted in the annotation of a large number of genes encoding proteins with an N-terminal signal peptide. This set is collectively referred to as the secretome and comprises proteins involved in, for example, cell wall growth and modification, proteolytic processes, and the promotion of successful invasion of plant cells. So far, proteomic profiling in oomycetes was primarily focused on subcellular, intracellular or cell wall fractions; the extracellular proteome has not been studied systematically. Here we present the first comprehensive characterization of the in vivo secretome and extracellular proteome of P. infestans. We have used mass spectrometry to analyze P. infestans proteins present in seven different growth media with mycelial cultures and this resulted in the consistent identification of over two hundred proteins. Gene ontology classification pinpointed proteins involved in cell wall modifications, pathogenesis, defense responses, and proteolytic processes. Moreover, we found members of the RXLR and CRN effector families as well as several proteins lacking an obvious signal peptide. The latter were confirmed to be bona fide extracellular proteins and this suggests that, similar to other organisms, oomycetes exploit non-conventional secretion mechanisms to transfer certain proteins to the extracellular environment.
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Affiliation(s)
- Harold J G Meijer
- From the ‡Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Francesco M Mancuso
- §Proteomics Unit, Center of Genomics Regulation (CRG), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain; ¶Proteomics Unit, Universitat Pompeu Fabra (UPF), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Guadalupe Espadas
- §Proteomics Unit, Center of Genomics Regulation (CRG), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain; ¶Proteomics Unit, Universitat Pompeu Fabra (UPF), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Michael F Seidl
- From the ‡Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; ‖Centre for BioSystems Genomics, Droevendaalsesteeg, 16708 PB Wageningen, The Netherlands
| | - Cristina Chiva
- §Proteomics Unit, Center of Genomics Regulation (CRG), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain; ¶Proteomics Unit, Universitat Pompeu Fabra (UPF), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Francine Govers
- From the ‡Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; ‖Centre for BioSystems Genomics, Droevendaalsesteeg, 16708 PB Wageningen, The Netherlands
| | - Eduard Sabidó
- §Proteomics Unit, Center of Genomics Regulation (CRG), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain; ¶Proteomics Unit, Universitat Pompeu Fabra (UPF), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain;
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17
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Ferreira R, Vitorino R, Padrão AI, Espadas G, Mancuso FM, Moreira-Gonçalves D, Castro-Sousa G, Henriques-Coelho T, Oliveira PA, Barros AS, Duarte JA, Sabidó E, Amado F. Lifelong exercise training modulates cardiac mitochondrial phosphoproteome in rats. J Proteome Res 2014; 13:2045-55. [PMID: 24467267 DOI: 10.1021/pr4011926] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Moderate physical activity has traditionally been associated with the improvement of cardiac function and, consequently, with the extension of life span. Mitochondria play a key role in the adaptation of heart muscle to exercise-related metabolic demands. In order to disclose the molecular mechanisms underlying the beneficial effect of lifelong physical activity in cardiac function, we performed label-free quantitative mass spectrometry-based proteomics of Sprague-Dawley rat heart mitochondrial proteome and phosphoproteome. Our data revealed that 54 weeks of moderate treadmill exercise modulates the abundance of proteins involved in the generation of precursor metabolites and cellular respiration, suggesting an increase in carbohydrate oxidation-based metabolism. Moreover, from the 1335 phosphopeptides identified in this study, 6 phosphosites were exclusively assigned to heart mitochondria from sedentary rats and 17 to exercised animals, corresponding to 6 and 16 proteins, respectively. Most proteins exhibiting significant alterations in specific phosphorylation sites were involved in metabolism. Analysis of the acquired data led to the identification of several kinases potentially modulated by exercise training, which were selected for further validation. Indeed, higher protein abundance levels of RAF and p38 in mitochondria were confirmed to be modulated by sustained exercise. Our work describes the plasticity of heart mitochondria in response to long exercise programs manifested by the reprogramming of phosphoproteome and provides evidence for the kinases involved in the regulation of metabolic pathways and mitochondrial maintenance.
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Affiliation(s)
- Rita Ferreira
- QOPNA, Department of Chemistry and ¶School of Health Sciences, University of Aveiro , Aveiro 3810-193, Portugal
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Affiliation(s)
- Jakob Bunkenborg
- Department of Clinical Biochemistry, Copenhagen University Hospital Hvidovre, DK-2650 Hvidovre,
Denmark
| | | | - Henrik Molina
- Center for Genomic Regulation, 08003 Barcelona, Spain
- The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
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Borràs E, Espadas G, Mancuso FM, Maier T, Chiva C, Sabidó E. Integrative quantitation enables a comprehensive proteome comparison of two Mycoplasma pneumoniae genetic perturbations. Mol BioSyst 2013; 9:1249-56. [DOI: 10.1039/c3mb25581f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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García-Santamarina S, Boronat S, Espadas G, Ayté J, Molina H, Hidalgo E. The oxidized thiol proteome in fission yeast—Optimization of an ICAT-based method to identify H2O2-oxidized proteins. J Proteomics 2011; 74:2476-86. [DOI: 10.1016/j.jprot.2011.05.030] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 04/19/2011] [Accepted: 05/20/2011] [Indexed: 10/18/2022]
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