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Jimenez-Marin A, Diez I, Erramuzpe A, Stramaglia S, Bonifazi P, Cortes JM. Open datasets and code for multi-scale relations on structure, function and neuro-genetics in the human brain. Sci Data 2024; 11:256. [PMID: 38424112 PMCID: PMC10904384 DOI: 10.1038/s41597-024-03060-2] [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: 08/10/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
The human brain is an extremely complex network of structural and functional connections that operate at multiple spatial and temporal scales. Investigating the relationship between these multi-scale connections is critical to advancing our comprehension of brain function and disorders. However, accurately predicting structural connectivity from its functional counterpart remains a challenging pursuit. One of the major impediments is the lack of public repositories that integrate structural and functional networks at diverse resolutions, in conjunction with modular transcriptomic profiles, which are essential for comprehensive biological interpretation. To mitigate this limitation, our contribution encompasses the provision of an open-access dataset consisting of derivative matrices of functional and structural connectivity across multiple scales, accompanied by code that facilitates the investigation of their interrelations. We also provide additional resources focused on neuro-genetic associations of module-level network metrics, which present promising opportunities to further advance research in the field of network neuroscience, particularly concerning brain disorders.
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Affiliation(s)
- Antonio Jimenez-Marin
- Computational Neuroimaging Lab, Biobizkaia HRI, Barakaldo, Spain
- Biomedical Research Doctorate Program, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Ibai Diez
- Department of Radiology, Division of Nuclear Medicine and Molecular Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, United States of America
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, United States of America
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, United States of America
| | - Asier Erramuzpe
- Computational Neuroimaging Lab, Biobizkaia HRI, Barakaldo, Spain
- IKERBASQUE Basque Foundation for Science, Bilbao, Spain
| | - Sebastiano Stramaglia
- Dipartamento Interateneo di Fisica, Universita Degli Studi di Bari Aldo Moro, INFN, Bari, Italy
| | - Paolo Bonifazi
- Computational Neuroimaging Lab, Biobizkaia HRI, Barakaldo, Spain
- IKERBASQUE Basque Foundation for Science, Bilbao, Spain
| | - Jesus M Cortes
- Computational Neuroimaging Lab, Biobizkaia HRI, Barakaldo, Spain.
- IKERBASQUE Basque Foundation for Science, Bilbao, Spain.
- Department of Cell Biology and Histology, University of the Basque Country (UPV/EHU), Leioa, Spain.
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2
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Torices L, Nunes-Xavier CE, Mingo J, Luna S, Erramuzpe A, Cortés JM, Pulido R. Induction of Translational Readthrough on Protein Tyrosine Phosphatases Targeted by Premature Termination Codon Mutations in Human Disease. Methods Mol Biol 2024; 2743:1-19. [PMID: 38147205 DOI: 10.1007/978-1-0716-3569-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Nonsense mutations generating premature termination codons (PTCs) in various genes are frequently associated with somatic cancer and hereditary human diseases since PTCs commonly generate truncated proteins with defective or altered function. Induced translational readthrough during protein biosynthesis facilitates the incorporation of an amino acid at the position of a PTC, allowing the synthesis of a complete protein. This may evade the pathological effect of the PTC mutation and provide new therapeutic opportunities. Several protein tyrosine phosphatases (PTPs) genes are targeted by PTC in human disease, the tumor suppressor PTEN being the more prominent paradigm. Here, using PTEN and laforin as examples, two PTPs from the dual-specificity phosphatase subfamily, we describe methodologies to analyze in silico the distribution and frequency of pathogenic PTC in PTP genes. We also summarize laboratory protocols and technical notes to study the induced translational readthrough reconstitution of the synthesis of PTP targeted by PTC in association with disease in cellular models.
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Affiliation(s)
- Leire Torices
- Biobizkaia Health Research Institute, Barakaldo, Spain
| | - Caroline E Nunes-Xavier
- Biobizkaia Health Research Institute, Barakaldo, Spain
- Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Janire Mingo
- Biobizkaia Health Research Institute, Barakaldo, Spain
| | - Sandra Luna
- Biobizkaia Health Research Institute, Barakaldo, Spain
| | - Asier Erramuzpe
- Biobizkaia Health Research Institute, Barakaldo, Spain
- Ikerbasque, The Basque Foundation for Science, Bilbao, Spain
| | - Jesús M Cortés
- Biobizkaia Health Research Institute, Barakaldo, Spain
- Ikerbasque, The Basque Foundation for Science, Bilbao, Spain
- Cell Biology and Histology Department, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Rafael Pulido
- Biobizkaia Health Research Institute, Barakaldo, Spain.
- Ikerbasque, The Basque Foundation for Science, Bilbao, Spain.
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3
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Romero-Bascones D, Ayala U, Alberdi A, Erramuzpe A, Galdós M, Gómez-Esteban JC, Murueta-Goyena A, Teijeira S, Gabilondo I, Barrenechea M. Spatial characterization of the effect of age and sex on macular layer thicknesses and foveal pit morphology. PLoS One 2022; 17:e0278925. [PMID: 36520804 PMCID: PMC9754220 DOI: 10.1371/journal.pone.0278925] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022] Open
Abstract
Characterizing the effect of age and sex on macular retinal layer thicknesses and foveal pit morphology is crucial to differentiating between natural and disease-related changes. We applied advanced image analysis techniques to optical coherence tomography (OCT) to: 1) enhance the spatial description of age and sex effects, and 2) create a detailed open database of normative retinal layer thickness maps and foveal pit shapes. The maculae of 444 healthy subjects (age range 21-88) were imaged with OCT. Using computational spatial data analysis, thickness maps were obtained for retinal layers and averaged into 400 (20 x 20) sectors. Additionally, the geometry of the foveal pit was radially analyzed by computing the central foveal thickness, rim height, rim radius, and mean slope. The effect of age and sex on these parameters was analyzed with multiple regression mixed-effects models. We observed that the overall age-related decrease of the total retinal thickness (TRT) (-1.1% per 10 years) was mainly driven by the ganglion cell-inner plexiform layer (GCIPL) (-2.4% per 10 years). Both TRT and GCIPL thinning patterns were homogeneous across the macula when using percentual measurements. Although the male retina was 4.1 μm thicker on average, the greatest differences were mainly present for the inner retinal layers in the inner macular ring (up to 4% higher TRT than in the central macula). There was an age-related decrease in the rim height (1.0% per 10 years) and males had a higher rim height, shorter rim radius, and steeper mean slope. Importantly, the radial analysis revealed that these changes are present and relatively uniform across angular directions. These findings demonstrate the capacity of advanced analysis of OCT images to enhance the description of the macula. This, together with the created dataset, could aid the development of more accurate diagnosis models for macular pathologies.
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Affiliation(s)
- David Romero-Bascones
- Biomedical Engineering Department, Faculty of Engineering (MU-ENG), Mondragon Unibertsitatea, Mondragón, Spain
| | - Unai Ayala
- Biomedical Engineering Department, Faculty of Engineering (MU-ENG), Mondragon Unibertsitatea, Mondragón, Spain
| | - Ane Alberdi
- Biomedical Engineering Department, Faculty of Engineering (MU-ENG), Mondragon Unibertsitatea, Mondragón, Spain
| | - Asier Erramuzpe
- Biomedical Engineering Department, Faculty of Engineering (MU-ENG), Mondragon Unibertsitatea, Mondragón, Spain
| | - Marta Galdós
- Ophthalmology Department, Cruces University Hospital, Barakaldo, Spain
| | - Juan Carlos Gómez-Esteban
- Neurodegenerative Disease Research Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Ane Murueta-Goyena
- Neurodegenerative Disease Research Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Neurosciences, Faculty of Medicine and Nursery, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Sara Teijeira
- Neurodegenerative Disease Research Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Iñigo Gabilondo
- Neurodegenerative Disease Research Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Ikerbasque, The Basque Foundation for Science, Bilbao, Spain
| | - Maitane Barrenechea
- Biomedical Engineering Department, Faculty of Engineering (MU-ENG), Mondragon Unibertsitatea, Mondragón, Spain
- * E-mail:
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Nunez-Ibero M, Camino-Pontes B, Diez I, Erramuzpe A, Martinez-Gutierrez E, Stramaglia S, Alvarez-Cienfuegos JO, Cortes JM. A Controlled Thermoalgesic Stimulation Device for Exploring Novel Pain Perception Biomarkers. IEEE J Biomed Health Inform 2021; 25:2948-2957. [PMID: 33999827 DOI: 10.1109/jbhi.2021.3080935] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
OBJECTIVE To develop a new device for identifying physiological markers of pain perception by reading the brain's electrical activity and hemodynamic interactions while applying thermoalgesic stimulation. METHODS We designed a compact prototype that generates well-controlled thermal stimuli using a computer-driven Peltier cell while simultaneously capturing electroencephalography (EEG) and photoplethysmography (PPG) signals. The study was performed on 35 healthy subjects (mean age 30.46 years, SD 4.93 years; 20 males, 15 females). We first determined the heat pain threshold (HPT) for each subject, defined as the maximum temperature that the subject can withstand when the Peltier cell gradually increased the temperature. Next, we defined the painful condition as the one occurring at temperature equal to 90% of the HPT, comparing this to the no-pain state (control) in the absence of thermoalgesic stimulation. RESULTS Both the one-dimensional and the two-dimensional spectral entropy (SE) obtained from both the EEG and PPG signals differentiated the condition of pain. In particular, the SE for PPG was significantly reduced in association with pain, while the SE for EEG increased slightly. Moreover, significant discrimination occurred within a specific range of frequencies, 26-30 Hz for EEG and about 5-10 Hz for PPG. CONCLUSION Hemodynamics, brain dynamics and their interactions can discriminate thermal pain perception. SIGNIFICANCE The possibility of monitoring on-line variations in thermal pain perception using a similar device and algorithms may be of interest to study different pathologies that affect the peripheral nervous system, such as small fiber neuropathies, fibromyalgia or painful diabetic neuropathy.
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Murueta-Goyena A, Barrenechea M, Erramuzpe A, Teijeira-Portas S, Pengo M, Ayala U, Romero-Bascones D, Acera M, Del Pino R, Gómez-Esteban JC, Gabilondo I. Foveal Remodeling of Retinal Microvasculature in Parkinson's Disease. Front Neurosci 2021; 15:708700. [PMID: 34321998 PMCID: PMC8311167 DOI: 10.3389/fnins.2021.708700] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/11/2021] [Indexed: 11/26/2022] Open
Abstract
Background Retinal microvascular alterations have been previously described in Parkinson’s disease (PD) patients using optical coherence tomography angiography (OCT-A). However, an extensive description of retinal vascular morphological features, their association with PD-related clinical variables and their potential use as diagnostic biomarkers has not been explored. Methods We performed a cross-sectional study including 49 PD patients (87 eyes) and 40 controls (73 eyes). Retinal microvasculature was evaluated with Spectralis OCT-A and cognitive status with Montreal Cognitive Assessment. Unified PD Rating Scale and disease duration were recorded in patients. We extracted microvascular parameters from superficial and deep vascular plexuses of the macula, including the area and circularity of foveal avascular zone (FAZ), skeleton density, perfusion density, vessel perimeter index, vessel mean diameter, fractal dimension (FD) and lacunarity using Python and MATLAB. We compared the microvascular parameters between groups and explored their association with thickness of macular layers and clinical outcomes. Data were analyzed with General Estimating Equations (GEE) and adjusted for age, sex, and hypertension. Logistic regression GEE models were fitted to predict diagnosis of PD versus controls from microvascular, demographic, and clinical data. The discrimination ability of models was tested with receiver operating characteristic curves. Results FAZ area was significantly smaller in patients compared to controls in superficial and deep plexuses, whereas perfusion density, skeleton density, FD and lacunarity of capillaries were increased in the foveal zone of PD. In the parafovea, microvascular parameters of superficial plexus were associated with ganglion cell-inner plexiform layer thickness, but this was mainly driven by PD with mild cognitive impairment. No such associations were observed in controls. FAZ area was negatively associated with cognition in PD (non-adjusted models). Foveal lacunarity, combined with demographic and clinical confounding factors, yielded an outstanding diagnostic accuracy for discriminating PD patients from controls. Conclusion Parkinson’s disease patients displayed foveal microvascular alterations causing an enlargement of the vascular bed surrounding FAZ. Parafoveal microvascular alterations were less pronounced but were related to inner retinal layer thinning. Retinal microvascular abnormalities helped discriminating PD from controls. All this supports OCT-A as a potential non-invasive biomarker to reveal vascular pathophysiology and improve diagnostic accuracy in PD.
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Affiliation(s)
- Ane Murueta-Goyena
- Neurodegenerative Diseases Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Department of Preventive Medicine and Public Health, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Maitane Barrenechea
- Biomedical Engineering Department, Faculty of Engineering, Mondragon Unibertsitatea (MU-ENG), Mondragon, Spain
| | - Asier Erramuzpe
- Biomedical Engineering Department, Faculty of Engineering, Mondragon Unibertsitatea (MU-ENG), Mondragon, Spain
| | - Sara Teijeira-Portas
- Neurodegenerative Diseases Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Marta Pengo
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Unai Ayala
- Biomedical Engineering Department, Faculty of Engineering, Mondragon Unibertsitatea (MU-ENG), Mondragon, Spain
| | - David Romero-Bascones
- Biomedical Engineering Department, Faculty of Engineering, Mondragon Unibertsitatea (MU-ENG), Mondragon, Spain
| | - Marian Acera
- Neurodegenerative Diseases Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Rocío Del Pino
- Neurodegenerative Diseases Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Juan Carlos Gómez-Esteban
- Neurodegenerative Diseases Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Neurology Department, Cruces University Hospital, Barakaldo, Spain.,Department of Neurosciences, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Iñigo Gabilondo
- Neurodegenerative Diseases Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Neurology Department, Cruces University Hospital, Barakaldo, Spain.,Ikerbasque: The Basque Foundation for Science, Bilbao, Spain
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6
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Sánchez-Puelles C, Calleja-Felipe M, Ouro A, Bougamra G, Arroyo A, Diez I, Erramuzpe A, Cortés J, Martínez-Hernández J, Luján R, Navarrete M, Venero C, Chan A, Morales M, Esteban JA, Knafo S. PTEN Activity Defines an Axis for Plasticity at Cortico-Amygdala Synapses and Influences Social Behavior. Cereb Cortex 2021; 30:505-524. [PMID: 31240311 DOI: 10.1093/cercor/bhz103] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 12/17/2018] [Revised: 03/29/2019] [Accepted: 04/25/2019] [Indexed: 12/11/2022] Open
Abstract
Phosphatase and tensin homolog on chromosome 10 (PTEN) is a tumor suppressor and autism-associated gene that exerts an important influence over neuronal structure and function during development. In addition, it participates in synaptic plasticity processes in adulthood. As an attempt to assess synaptic and developmental mechanisms by which PTEN can modulate cognitive function, we studied the consequences of 2 different genetic manipulations in mice: presence of additional genomic copies of the Pten gene (Ptentg) and knock-in of a truncated Pten gene lacking its PDZ motif (Pten-ΔPDZ), which is required for interaction with synaptic proteins. Ptentg mice exhibit substantial microcephaly, structural hypoconnectivity, enhanced synaptic depression at cortico-amygdala synapses, reduced anxiety, and intensified social interactions. In contrast, Pten-ΔPDZ mice have a much more restricted phenotype, with normal synaptic connectivity, but impaired synaptic depression at cortico-amygdala synapses and virtually abolished social interactions. These results suggest that synaptic actions of PTEN in the amygdala contribute to specific behavioral traits, such as sociability. Also, PTEN appears to function as a bidirectional rheostat in the amygdala: reduction in PTEN activity at synapses is associated with less sociability, whereas enhanced PTEN activity accompanies hypersocial behavior.
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Affiliation(s)
- Cristina Sánchez-Puelles
- Molecular Cognition Laboratory, Biophysics Institute, Consejo Superior de Investigaciones Cientificas (CSIC)-University of the Basque Country (UPV)/Euskal Herriko University (EHU), Campus Universidad del País Vasco, 48940 Leioa, Spain.,Department of Molecular Neurobiology, Centro de Biología Molecular Severo Ochoa, CSIC/Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - María Calleja-Felipe
- Molecular Cognition Laboratory, Biophysics Institute, Consejo Superior de Investigaciones Cientificas (CSIC)-University of the Basque Country (UPV)/Euskal Herriko University (EHU), Campus Universidad del País Vasco, 48940 Leioa, Spain
| | - Alberto Ouro
- Molecular Cognition Laboratory, Biophysics Institute, Consejo Superior de Investigaciones Cientificas (CSIC)-University of the Basque Country (UPV)/Euskal Herriko University (EHU), Campus Universidad del País Vasco, 48940 Leioa, Spain
| | - Ghassen Bougamra
- Molecular Cognition Laboratory, Biophysics Institute, Consejo Superior de Investigaciones Cientificas (CSIC)-University of the Basque Country (UPV)/Euskal Herriko University (EHU), Campus Universidad del País Vasco, 48940 Leioa, Spain
| | - Ana Arroyo
- Molecular Cognition Laboratory, Biophysics Institute, Consejo Superior de Investigaciones Cientificas (CSIC)-University of the Basque Country (UPV)/Euskal Herriko University (EHU), Campus Universidad del País Vasco, 48940 Leioa, Spain
| | - Ibai Diez
- Computational Neuroimaging Laboratory, Biocruces Health Research Institute, 48903 Barakaldo, Spain
| | - Asier Erramuzpe
- Computational Neuroimaging Laboratory, Biocruces Health Research Institute, 48903 Barakaldo, Spain
| | - Jesús Cortés
- Computational Neuroimaging Laboratory, Biocruces Health Research Institute, 48903 Barakaldo, Spain.,Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - José Martínez-Hernández
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Rafael Luján
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Marta Navarrete
- Department of Molecular Neurobiology, Centro de Biología Molecular Severo Ochoa, CSIC/Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - César Venero
- Department of Psychobiology, Universidad Nacional de Educación a Distancia, 28040 Madrid, Spain
| | - Andrew Chan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Miguel Morales
- Molecular Cognition Laboratory, Biophysics Institute, Consejo Superior de Investigaciones Cientificas (CSIC)-University of the Basque Country (UPV)/Euskal Herriko University (EHU), Campus Universidad del País Vasco, 48940 Leioa, Spain
| | - José A Esteban
- Department of Molecular Neurobiology, Centro de Biología Molecular Severo Ochoa, CSIC/Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Shira Knafo
- Molecular Cognition Laboratory, Biophysics Institute, Consejo Superior de Investigaciones Cientificas (CSIC)-University of the Basque Country (UPV)/Euskal Herriko University (EHU), Campus Universidad del País Vasco, 48940 Leioa, Spain.,Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain.,Department of Physiology and Cell Biology and National Institute of Biotechnology in the Negev, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 8410501 Israel
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7
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Luna S, Torices L, Mingo J, Amo L, Rodríguez-Escudero I, Ruiz-Ibarlucea P, Erramuzpe A, Cortés JM, Tejada MI, Molina M, Nunes-Xavier CE, López JI, Cid VJ, Pulido R. A global analysis of the reconstitution of PTEN function by translational readthrough of PTEN pathogenic premature termination codons. Hum Mutat 2021; 42:551-566. [PMID: 33600059 DOI: 10.1002/humu.24186] [Citation(s) in RCA: 7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/15/2021] [Accepted: 02/14/2021] [Indexed: 12/29/2022]
Abstract
The PTEN tumor suppressor gene is mutated with high incidence in tumors and in the germline of patients with cancer predisposition or with macrocephaly associated with autism. PTEN nonsense mutations generating premature termination codons (PTC) and producing nonfunctional truncated PTEN proteins are frequent in association with human disease. However, there are no studies addressing the restoration of full-length PTEN proteins from the PTC-mutated PTEN gene by translational readthrough. Here, we have performed a global translational and functional readthrough analysis of the complete collection of PTEN PTC somatic or hereditary mutations found in tumors or in the germline of patients (disease-associated PTEN PTCome), and we set standards for the analysis of the potential of readthrough functional reconstitution in disease-relevant genes. Our analysis indicates that prevalent pathogenic PTEN PTC mutations are susceptible to PTEN functional restoration in response to readthrough-inducing compounds. Comprehensive readthrough analyses of disease-associated PTComes will be valuable tools for the implementation of readthrough-based precision interventions in specific groups of patients.
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Affiliation(s)
- Sandra Luna
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Leire Torices
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Janire Mingo
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Laura Amo
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Isabel Rodríguez-Escudero
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, UCM & Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, Spain
| | | | - Asier Erramuzpe
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Jesús M Cortés
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Ikerbasque, The Basque Foundation for Science, Bilbao, Spain
| | - María I Tejada
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - María Molina
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, UCM & Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, Spain
| | - Caroline E Nunes-Xavier
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - José I López
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Department of Pathology, Cruces University Hospital, Barakaldo, Spain
| | - Víctor J Cid
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, UCM & Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, Spain
| | - Rafael Pulido
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Ikerbasque, The Basque Foundation for Science, Bilbao, Spain
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8
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Erramuzpe A, Schurr R, Yeatman JD, Gotlib IH, Sacchet MD, Travis KE, Feldman HM, Mezer AA. A Comparison of Quantitative R1 and Cortical Thickness in Identifying Age, Lifespan Dynamics, and Disease States of the Human Cortex. Cereb Cortex 2021; 31:1211-1226. [PMID: 33095854 PMCID: PMC8485079 DOI: 10.1093/cercor/bhaa288] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 05/15/2020] [Revised: 08/25/2020] [Accepted: 09/03/2020] [Indexed: 07/22/2023] Open
Abstract
Brain development and aging are complex processes that unfold in multiple brain regions simultaneously. Recently, models of brain age prediction have aroused great interest, as these models can potentially help to understand neurological diseases and elucidate basic neurobiological mechanisms. We test whether quantitative magnetic resonance imaging can contribute to such age prediction models. Using R1, the longitudinal rate of relaxation, we explore lifespan dynamics in cortical gray matter. We compare R1 with cortical thickness, a well-established biomarker of brain development and aging. Using 160 healthy individuals (6-81 years old), we found that R1 and cortical thickness predicted age similarly, but the regions contributing to the prediction differed. Next, we characterized R1 development and aging dynamics. Compared with anterior regions, in posterior regions we found an earlier R1 peak but a steeper postpeak decline. We replicate these findings: firstly, we tested a subset (N = 10) of the original dataset for whom we had additional scans at a lower resolution; and second, we verified the results on an independent dataset (N = 34). Finally, we compared the age prediction models on a subset of 10 patients with multiple sclerosis. The patients are predicted older than their chronological age using R1 but not with cortical thickness.
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Affiliation(s)
| | - R Schurr
- The Hebrew University of Jerusalem, The Edmond and Lily Safra Center for Brain Sciences, Jerusalem, Israel
| | - J D Yeatman
- Graduate School of Education, Stanford University, Stanford, CA, USA
- Division of Developmental-Behavioral Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - I H Gotlib
- Psychology, Stanford University, Stanford, CA, USA
| | - M D Sacchet
- Harvard Medical School, Center for Depression, Anxiety, and Stress Research, McLean Hospital, Belmont, MA, USA
| | - K E Travis
- Pediatrics, Stanford University, Stanford, CA, USA
| | - H M Feldman
- Development and Behavior Unit, Stanford University, Stanford, CA, USA
| | - A A Mezer
- The Hebrew University of Jerusalem, The Edmond and Lily Safra Center for Brain Sciences, Jerusalem, Israel
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9
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Abstract
Abstract: Background: Recent findings on retrieval of proper names in cognitively healthy middle-aged persons indicate that Tip-Of-The-Tongue (TOT) states occurring during proper name retrieval implicate inferior frontal (BA 44) and parietal (BA 40) cortical areas. Such findings give rise to the possibility that anatomical connectivity via dorsal white matter may be associated with difficulties in name retrieval in midlife. Objectives & Method: Using Diffusion Tensor Imaging, we examined in vivo microstructural properties of white matter in 72 cognitively healthy Middle-Aged (MA) and 59 Young Adults (YA), comparing their naming abilities as well as testing, for possible associations between dorsal white matter integrity and naming abilities in the MA group. Results: The MA group was better in retrieving correct names (U = 1525.5, p = .006), but they also retrieved more incorrect names than YA believing they had retrieved the correct ones (U = 1265.5, p < .001). Furthermore, despite being more familiar with the tested names than YA (U = 930, p < .001), MA experienced significantly more TOTs relative to YA (U = 1498.5, p = .004). Tract-based spatial statistics showed significant group differences in values of fractional anisotropy (FA), mean diffusivity, axial diffusivity, radial diffusivity, and mode of anisotropy in a range of white matter tracts. In the MA group, FA values in the right Superior Longitudinal Fasciculus (SLF) were positively correlated with “don’t know” scores (rs = .287, p = .014). Conclusion: The association of SLF integrity and name retrieval ability in midlife indicates a need to revisit the models of name retrieval that posit no role for dorsal white matter in proper name retrieval.
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He C, Chen H, Uddin LQ, Erramuzpe A, Bonifazi P, Guo X, Xiao J, Chen H, Huang X, Li L, Sheng W, Liao W, Cortes JM, Duan X. Structure-Function Connectomics Reveals Aberrant Developmental Trajectory Occurring at Preadolescence in the Autistic Brain. Cereb Cortex 2020; 30:5028-5037. [PMID: 32377684 PMCID: PMC7391416 DOI: 10.1093/cercor/bhaa098] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/08/2020] [Accepted: 03/25/2020] [Indexed: 12/25/2022] Open
Abstract
Accumulating neuroimaging evidence shows that age estimation obtained from brain connectomics reflects the level of brain maturation along with neural development. It is well known that autism spectrum disorder (ASD) alters neurodevelopmental trajectories of brain connectomics, but the precise relationship between chronological age (ChA) and brain connectome age (BCA) during development in ASD has not been addressed. This study uses neuroimaging data collected from 50 individuals with ASD and 47 age- and gender-matched typically developing controls (TDCs; age range: 5-18 years). Both functional and structural connectomics were assessed using resting-state functional magnetic resonance imaging and diffusion tensor imaging data from the Autism Brain Imaging Data Exchange repository. For each participant, BCA was estimated from structure-function connectomics through linear support vector regression. We found that BCA matched well with ChA in TDC children and adolescents, but not in ASD. In particular, our findings revealed that individuals with ASD exhibited accelerated brain maturation in youth, followed by a delay of brain development starting at preadolescence. Our results highlight the critical role of BCA in understanding aberrant developmental trajectories in ASD and provide the new insights into the pathophysiological mechanisms of this disorder.
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Affiliation(s)
- Changchun He
- Department of Life Science and Technology, The clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu 610054, China
- MOE Key Lab for Neuroinformation, High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Huafu Chen
- Department of Life Science and Technology, The clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu 610054, China
- MOE Key Lab for Neuroinformation, High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Lucina Q Uddin
- Department of Psychology, University of Miami, Coral Gables, FL 33124, USA
| | - Asier Erramuzpe
- Computational Neuroimaging Laboratory, Biocruces-Bizkaia Health Research Institute, Barakaldo 48903, Spain
- Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91905, Israel
| | - Paolo Bonifazi
- Computational Neuroimaging Laboratory, Biocruces-Bizkaia Health Research Institute, Barakaldo 48903, Spain
- Ikerbasque: The Basque Foundation for Science, Bilbao 48013, Spain
| | - Xiaonan Guo
- Department of Life Science and Technology, The clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu 610054, China
- MOE Key Lab for Neuroinformation, High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Jinming Xiao
- Department of Life Science and Technology, The clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu 610054, China
- MOE Key Lab for Neuroinformation, High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Heng Chen
- School of Medicine, Medical College of Guizhou University, Guiyang 550025, China
| | - Xinyue Huang
- Department of Life Science and Technology, The clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu 610054, China
- MOE Key Lab for Neuroinformation, High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Lei Li
- Department of Life Science and Technology, The clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu 610054, China
- MOE Key Lab for Neuroinformation, High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Wei Sheng
- Department of Life Science and Technology, The clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu 610054, China
- MOE Key Lab for Neuroinformation, High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Wei Liao
- Department of Life Science and Technology, The clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu 610054, China
- MOE Key Lab for Neuroinformation, High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Jesus M Cortes
- Ikerbasque: The Basque Foundation for Science, Bilbao 48013, Spain
- Department of Cell Biology and Histology, University of the Basque Country, Leioa, Spain
| | - Xujun Duan
- Department of Life Science and Technology, The clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu 610054, China
- MOE Key Lab for Neuroinformation, High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, University of Electronic Science and Technology of China, Chengdu 610054, China
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11
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Sánchez-Puelles C, Calleja-Felipe M, Ouro A, Bougamra G, Arroyo A, Diez I, Erramuzpe A, Cortés J, Martínez-Hernández J, Luján R, Navarrete M, Venero C, Chan A, Morales M, Esteban JA, Knafo S. Corrigendum to: -PTEN activity defines an axis for plasticity at cortico-amygdala synapses and influences social behavior. Cereb Cortex 2020; 30:849. [PMID: 31560052 DOI: 10.1093/cercor/bhz232] [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] [Received: 12/17/2018] [Revised: 03/29/2019] [Accepted: 04/25/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Cristina Sánchez-Puelles
- Molecular Cognition Laboratory, Biophysics Institute, Consejo Superior de Investigaciones Cientificas (CSIC)-University of the Basque Country (UPV)/Euskal Herriko University (EHU), Campus Universidad del País Vasco, 48940 Leioa, Spain.,Department of Molecular Neurobiology, Centro de Biología Molecular Severo Ochoa, CSIC/Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Instituto Cajal, CSIC, 28002 Madrid, Spain
| | - María Calleja-Felipe
- Molecular Cognition Laboratory, Biophysics Institute, Consejo Superior de Investigaciones Cientificas (CSIC)-University of the Basque Country (UPV)/Euskal Herriko University (EHU), Campus Universidad del País Vasco, 48940 Leioa, Spain
| | - Alberto Ouro
- Molecular Cognition Laboratory, Biophysics Institute, Consejo Superior de Investigaciones Cientificas (CSIC)-University of the Basque Country (UPV)/Euskal Herriko University (EHU), Campus Universidad del País Vasco, 48940 Leioa, Spain
| | - Ghassen Bougamra
- Molecular Cognition Laboratory, Biophysics Institute, Consejo Superior de Investigaciones Cientificas (CSIC)-University of the Basque Country (UPV)/Euskal Herriko University (EHU), Campus Universidad del País Vasco, 48940 Leioa, Spain
| | - Ana Arroyo
- Molecular Cognition Laboratory, Biophysics Institute, Consejo Superior de Investigaciones Cientificas (CSIC)-University of the Basque Country (UPV)/Euskal Herriko University (EHU), Campus Universidad del País Vasco, 48940 Leioa, Spain
| | - Ibai Diez
- Computational Neuroimaging Laboratory, Biocruces Health Research Institute, 48903 Barakaldo, Spain
| | - Asier Erramuzpe
- Computational Neuroimaging Laboratory, Biocruces Health Research Institute, 48903 Barakaldo, Spain
| | - Jesús Cortés
- Computational Neuroimaging Laboratory, Biocruces Health Research Institute, 48903 Barakaldo, Spain.,Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - José Martínez-Hernández
- Synaptic Structure Laboratory, Instituto de Investigación en Discapacidades Neurológicas, Departamento Ciencias Médicas, Facultad de Medicina, Universidad Castilla-La Mancha, 02008 Albacete, Spain
| | - Rafael Luján
- Synaptic Structure Laboratory, Instituto de Investigación en Discapacidades Neurológicas, Departamento Ciencias Médicas, Facultad de Medicina, Universidad Castilla-La Mancha, 02008 Albacete, Spain
| | - Marta Navarrete
- Department of Molecular Neurobiology, Centro de Biología Molecular Severo Ochoa, CSIC/Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Instituto Cajal, CSIC, 28002 Madrid, Spain
| | - César Venero
- Department of Psychobiology, Universidad Nacional de Educación a Distancia, 28040 Madrid, Spain
| | - Andrew Chan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Miguel Morales
- Molecular Cognition Laboratory, Biophysics Institute, Consejo Superior de Investigaciones Cientificas (CSIC)-University of the Basque Country (UPV)/Euskal Herriko University (EHU), Campus Universidad del País Vasco, 48940 Leioa, Spain
| | - José A Esteban
- Department of Molecular Neurobiology, Centro de Biología Molecular Severo Ochoa, CSIC/Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Shira Knafo
- Molecular Cognition Laboratory, Biophysics Institute, Consejo Superior de Investigaciones Cientificas (CSIC)-University of the Basque Country (UPV)/Euskal Herriko University (EHU), Campus Universidad del País Vasco, 48940 Leioa, Spain.,Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain.,Department of Physiology and Cell Biology and National Institute of Biotechnology in the Negev, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 8410501 Israel
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12
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Nunes-Xavier CE, Aurtenetxe O, Zaldumbide L, López-Almaraz R, Erramuzpe A, Cortés JM, López JI, Pulido R. Protein tyrosine phosphatase PTPN1 modulates cell growth and associates with poor outcome in human neuroblastoma. Diagn Pathol 2019; 14:134. [PMID: 31837707 PMCID: PMC6911276 DOI: 10.1186/s13000-019-0919-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 12/06/2019] [Indexed: 02/08/2023] Open
Abstract
Background Protein tyrosine phosphatases (PTPs) regulate neuronal differentiation and survival, but their expression patterns and functions in human neuroblastoma (NB) are scarcely known. Here, we have investigated the function and expression of the non-receptor PTPN1 on human NB cell lines and human NB tumor samples. Material/methods NB tumor samples from 44 patients were analysed by immunohistochemistry using specific antibodies against PTPN1, PTPRH, PTPRZ1, and PTEN. PTPN1 knock-down, cell proliferation and tyrosine phosphorylation analyses, and RT-qPCR mRNA expression was assessed on SH-SY5Y, SMS-KCNR, and IMR-32 human NB cell lines. Results Knock-down of PTPN1 in SH-SY5Y NB cells resulted in increased tyrosine phosphorylation and cell proliferation. Retinoic acid-mediated differentiation of NB cell lines did not affect PTPN1 mRNA expression, as compared with other PTPs. Importantly, PTPN1 displayed high expression on NB tumors in association with metastasis and poor prognosis. Conclusions Our results identify PTPN1 as a candidate regulator of NB cell growth and a potential NB prognostic biomarker.
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Affiliation(s)
- Caroline E Nunes-Xavier
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Bizkaia, Spain. .,Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, P.O. Box 4950 Nydalen, N-0424, Oslo, Norway.
| | - Olaia Aurtenetxe
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Bizkaia, Spain
| | - Laura Zaldumbide
- Department of Pathology, Cruces University Hospital, University of the Basque Country (UPV/EHU), Barakaldo, Bizkaia, Spain
| | - Ricardo López-Almaraz
- Pediatric Oncology and Hematology, Cruces University Hospital, Barakaldo, Bizkaia, Spain
| | - Asier Erramuzpe
- Quantitative Biomedicine Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Bizkaia, Spain
| | - Jesús M Cortés
- Quantitative Biomedicine Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Bizkaia, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - José I López
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Bizkaia, Spain.,Department of Pathology, Cruces University Hospital, University of the Basque Country (UPV/EHU), Barakaldo, Bizkaia, Spain
| | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Bizkaia, Spain. .,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain. .,Biocruces Bizkaia Health Research Institute, Hospital Universitario de Cruces, Plaza Cruces s/n, 48903, Barakaldo, Spain.
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13
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Fuertes MC, Aranda G, Rezola N, Erramuzpe A, Palacios C, Ibañez B. [Long-term effects of a mindfulness and self-compassion program with Primary Healthcare professionals]. An Sist Sanit Navar 2019; 42:269-280. [PMID: 31859274 DOI: 10.23938/assn.0718] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
BACKGROUND The effectiveness of mindfulness and self-compassion-based interventions (MSCI) on emotional fatigue and stress in Primary Healthcare (PHC) professionals has been demonstrated in the short term. The aims of this work were to assess whether these effects persist after two years, and if the observed results differ between those who practiced mindfulness regularly during the follow-up (meditators) and those who did not. METHODS Prospective study - pre-post and two years after performing an MSCI that was offered to all PHC professionals in Navarra, with group sessions of 2.5 hours / week for 8 weeks. Attending at least 75% of the sessions and practicing at home for 45 minutes a day were mandatory. At the three moments of the study, questionnaires were distributed to measure levels of mindfulness (FFMQ), self-compassion (SCS), perceived stress (PSQ) and burnout (MBI). At the end of the follow-up period, participants were asked if they were meditators and the time they dedicated to this weekly. RESULTS Forty-eight professionals were enrolled and 41 (83% women) met the inclusion criteria, without loss to follow-up. Mean scores in mindfulness, self-compassion and perceived stress significantly improved after the intervention and in the long term (p <0.001), without observing differences in the level of burnout. The group of meditators achieved a greater long-term improvement in self-compassion (3.6 points vs. 1.6). CONCLUSIONS The effectiveness of an MSCI persists two years later regardless of meditator status, although there is a significant improvement in self-compassion in the meditators.
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Affiliation(s)
- M C Fuertes
- Sección de Planificación. Departamento de Salud. Gobierno de Navarra. Pamplona..
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14
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Camino-Pontes B, Diez I, Jimenez-Marin A, Rasero J, Erramuzpe A, Bonifazi P, Stramaglia S, Swinnen S, Cortes JM. Interaction Information Along Lifespan of the Resting Brain Dynamics Reveals a Major Redundant Role of the Default Mode Network. Entropy (Basel) 2018; 20:e20100742. [PMID: 33265831 PMCID: PMC7512305 DOI: 10.3390/e20100742] [Citation(s) in RCA: 14] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/07/2018] [Accepted: 09/24/2018] [Indexed: 01/06/2023]
Abstract
Interaction Information (II) generalizes the univariate Shannon entropy to triplets of variables, allowing the detection of redundant (R) or synergetic (S) interactions in dynamical networks. Here, we calculated II from functional magnetic resonance imaging data and asked whether R or S vary across brain regions and along lifespan. Preserved along lifespan, we found high overlapping between the pattern of high R and the default mode network, whereas high values of S were overlapping with different cognitive domains, such as spatial and temporal memory, emotion processing and motor skills. Moreover, we have found a robust balance between R and S among different age intervals, indicating informational compensatory mechanisms in brain networks.
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Affiliation(s)
- Borja Camino-Pontes
- Computational Neuroimaging Lab, Biocruces Health Research Institute, 48903 Barakaldo, Spain
| | - Ibai Diez
- Functional Neurology Research Group, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Gordon Center, Department of Nuclear Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Neurotechnology Laboratory, Tecnalia Health Department, 48160 Derio, Spain
| | - Antonio Jimenez-Marin
- Computational Neuroimaging Lab, Biocruces Health Research Institute, 48903 Barakaldo, Spain
| | - Javier Rasero
- Computational Neuroimaging Lab, Biocruces Health Research Institute, 48903 Barakaldo, Spain
| | - Asier Erramuzpe
- Computational Neuroimaging Lab, Biocruces Health Research Institute, 48903 Barakaldo, Spain
| | - Paolo Bonifazi
- Computational Neuroimaging Lab, Biocruces Health Research Institute, 48903 Barakaldo, Spain
- IKERBASQUE: The Basque Foundation for Science, 48013 Bilbao, Spain
| | | | - Stephan Swinnen
- Movement Control and Neuroplasticity Research Group, Department of Movement Sciences, KU Leuven, 3001 Leuven, Belgium
- Leuven Brain Institute (LBI), KU Leuven, 3000 Leuven, Belgium
| | - Jesus M. Cortes
- Computational Neuroimaging Lab, Biocruces Health Research Institute, 48903 Barakaldo, Spain
- IKERBASQUE: The Basque Foundation for Science, 48013 Bilbao, Spain
- Department of Cell Biology and Histology, University of the Basque Country, 48940 Leioa, Spain
- Correspondence: ; Tel.: +34-94600600 (ext. 5199)
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15
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Bonifazi P, Erramuzpe A, Diez I, Gabilondo I, Boisgontier MP, Pauwels L, Stramaglia S, Swinnen SP, Cortes JM. Structure-function multi-scale connectomics reveals a major role of the fronto-striato-thalamic circuit in brain aging. Hum Brain Mapp 2018; 39:4663-4677. [PMID: 30004604 DOI: 10.1002/hbm.24312] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 06/27/2018] [Accepted: 06/28/2018] [Indexed: 12/15/2022] Open
Abstract
Physiological aging affects brain structure and function impacting morphology, connectivity, and performance. However, whether some brain connectivity metrics might reflect the age of an individual is still unclear. Here, we collected brain images from healthy participants (N = 155) ranging from 10 to 80 years to build functional (resting state) and structural (tractography) connectivity matrices, both data sets combined to obtain different connectivity features. We then calculated the brain connectome age-an age estimator resulting from a multi-scale methodology applied to the structure-function connectome, and compared it to the chronological age (ChA). Our results were twofold. First, we found that aging widely affects the connectivity of multiple structures, such as anterior cingulate and medial prefrontal cortices, basal ganglia, thalamus, insula, cingulum, hippocampus, parahippocampus, occipital cortex, fusiform, precuneus, and temporal pole. Second, we found that the connectivity between basal ganglia and thalamus to frontal areas, also known as the fronto-striato-thalamic (FST) circuit, makes the major contribution to age estimation. In conclusion, our results highlight the key role played by the FST circuit in the process of healthy aging. Notably, the same methodology can be generally applied to identify the structural-functional connectivity patterns correlating to other biomarkers than ChA.
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Affiliation(s)
- Paolo Bonifazi
- Biocruces Health Research Institute, Barakaldo, Spain.,IKERBASQUE: The Basque Foundation for Science, Bilbao, Spain
| | | | - Ibai Diez
- Biocruces Health Research Institute, Barakaldo, Spain
| | | | - Matthieu P Boisgontier
- Movement Control and Neuroplasticity Research Group, Department of Movement Sciences, Group Biomedical Sciences, KU Leuven, Leuven, Belgium
| | - Lisa Pauwels
- Movement Control and Neuroplasticity Research Group, Department of Movement Sciences, Group Biomedical Sciences, KU Leuven, Leuven, Belgium
| | - Sebastiano Stramaglia
- Dipartimento Interateneo di Fisica, Universita di Bari, and INFN, Sezione di Bari, Italy
| | - Stephan P Swinnen
- Movement Control and Neuroplasticity Research Group, Department of Movement Sciences, Group Biomedical Sciences, KU Leuven, Leuven, Belgium.,Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
| | - Jesus M Cortes
- Biocruces Health Research Institute, Barakaldo, Spain.,IKERBASQUE: The Basque Foundation for Science, Bilbao, Spain.,Department of Cell Biology and Histology, University of the Basque Country, Leioa, Spain
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16
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Kljajevic V, Erramuzpe A. Proper name retrieval and structural integrity of cerebral cortex in midlife: A cross-sectional study. Brain Cogn 2017; 120:26-33. [PMID: 29253727 DOI: 10.1016/j.bandc.2017.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 04/03/2017] [Revised: 11/20/2017] [Accepted: 11/21/2017] [Indexed: 11/20/2022]
Abstract
There is currently little understanding on whether retrieval of proper names differs in midlife compared to young adulthood and if so, whether the age differences in this ability are associated with differences in structural integrity of the cerebral cortex. To answer these questions, we studied retrieval of proper names in 115 cognitively healthy middle-aged persons (49.7, ±3.2), comparing their performance on a tip-of-the-tongue (TOT) task with that of 68 young persons (25.4, ±3.5) from the Cam-Can data repository (http://www.mrc-cbu.cam.ac.uk/datasets/camcan/). Grey matter (GM) density and cortical thickness were used as indices of structural integrity of the cerebral cortex. The middle-aged (MA) group experienced more TOTs during proper names retrieval than young adults (YA), (t = 3.789, p < .005) and had considerably less GM density and cortical thickness across a range of brain areas bilaterally. Small clusters in left BA 45 and right BA 44 (cortical thickness) and in right BA 40 (volumetry) revealed group differences when accounting for TOTs. However, we observed no correlations between MA's TOT scores and GM volumes or cortical thickness of the brain regions typically reported as implicated in retrieval of proper names: left anterior temporal lobe, left insula, and left superior and middle temporal gyri.
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Affiliation(s)
- Vanja Kljajevic
- University of the Basque Country, Vitoria, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
| | - Asier Erramuzpe
- BioCruces Health Research Institute, Cruces University Hospital, Barakaldo, Spain
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Lissek T, Adams M, Adelman J, Ahissar E, Akaaboune M, Akil H, al’Absi M, Arain F, Arango-Lasprilla JC, Atasoy D, Avila J, Badawi A, Bading H, Baig AM, Baleriola J, Belmonte C, Bertocchi I, Betz H, Blakemore C, Blanke O, Boehm-Sturm P, Bonhoeffer T, Bonifazi P, Brose N, Campolongo P, Celikel T, Chang CC, Chang TY, Citri A, Cline HT, Cortes JM, Cullen K, Dean K, Delgado-Garcia JM, Desroches M, Disterhoft JF, Dowling JE, Draguhn A, El-Khamisy SF, El Manira A, Enam SA, Encinas JM, Erramuzpe A, Esteban JA, Fariñas I, Fischer E, Fukunaga I, Gabilondo I, Ganten D, Gidon A, Gomez-Esteban JC, Greengard P, Grinevich V, Gruart A, Guillemin R, Hariri AR, Hassan B, Häusser M, Hayashi Y, Hussain NK, Jabbar AA, Jaber M, Jahn R, Janahi EM, Kabbaj M, Kettenmann H, Kindt M, Knafo S, Köhr G, Komai S, Krugers H, Kuhn B, Ghazal NL, Larkum ME, London M, Lutz B, Matute C, Martinez-Millan L, Maroun M, McGaugh J, Moustafa AA, Nasim A, Nave KA, Neher E, Nikolich K, Outeiro T, Palmer LM, Penagarikano O, Perez-Otano I, Pfaff DW, Poucet B, Rahman AU, Ramos-Cabrer P, Rashidy-Pour A, Roberts RJ, Rodrigues S, Sanes JR, Schaefer AT, Segal M, Segev I, Shafqat S, Siddiqui NA, Soreq H, Soriano-García E, Spanagel R, Sprengel R, Stuart G, Südhof TC, Tønnesen J, Treviño M, Uthman BM, Venter JC, Verkhratsky A, Weiss C, Wiesel TN, Yaksi E, Yizhar O, Young LJ, Young P, Zawia NH, Zugaza JL, Hasan MT. Building Bridges through Science. Neuron 2017; 96:730-735. [DOI: 10.1016/j.neuron.2017.09.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 09/16/2017] [Accepted: 09/19/2017] [Indexed: 10/18/2022]
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18
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Luna S, Mingo J, Amo L, Rodríguez-Escudero I, Erramuzpe A, Molina M, Nunes-Xavier C, Tejada I, López J, Cortés J, Cid V, Pulido R. Readthrough response of pathogenic premature termination codons at PTEN gene: implications in precision therapy for PHTS patients. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx508.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Pulido R, Aurtenetxe O, Zaldumbide L, Erramuzpe A, López R, López J, Cortés J, Nunes-Xavier C. Neuroblastoma PTPome analysis unveils association of DUSP5 and PTPN1 expression with poor prognosis. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx511.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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López JI, Erramuzpe A, Guarch R, Cortés JM, Pulido R, Llarena R, Angulo JC. CD34 immunostaining enhances a distinct pattern of intratumor angiogenesis with prognostic implications in clear cell renal cell carcinoma. APMIS 2017; 125:128-133. [PMID: 28120493 DOI: 10.1111/apm.12649] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/15/2016] [Indexed: 12/12/2022]
Abstract
Clear cell renal cell carcinoma is an aggressive neoplasm related to VHL gene inactivation. The molecular events derived from this initial alteration lead to a permanent intracellular pseudo-hypoxic status that stimulates vascular proliferation. The resulting increased intratumor angiogenesis is the target of most modern therapies. Although intratumor angiogenesis has received full attention in the last years, few studies have focused on its potential importance from a strict morphological approach. Intratumor angiogenesis has been analyzed in a retrospective series of clear cell renal cell carcinomas (n = 208) with long-term follow-up (n = 177). Two different patterns of angiogenesis have been highlighted with CD34 at the front of tumor invasion, termed continuous and discontinuous, respectively. The continuous pattern of angiogenesis showed a complete microvascular network surrounding totally tumor nests. Conversely, the discontinuous pattern displayed an incomplete network around tumor nests. The continuous pattern was associated to shorter 5-year (p = 0.00064, hazard ratio = 2.8) and 15-year (p = 0.014, hazard ratio = 1.7) survivals. Cox regression multivariate analysis also showed that the continuous pattern (p = 0.016373) remains a significant variable when considered together with grade (p = 0.001755) and stage (p = 0.000952). These findings support the notion that a continuous CD34+ pattern of intratumor angiogenesis may be useful for pathologists in predicting tumor behavior in clear cell renal cell carcinomas.
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Affiliation(s)
- José I López
- Department of Pathology, Cruces University Hospital, University of the Basque Country (UPV/EHU), Barakaldo, Bizkaia, Spain.,Biomarkers in Cancer Unit, BioCruces Health Research Institute, Barakaldo, Bizkaia, Spain
| | - Asier Erramuzpe
- Quantitative Biomedicine Unit, BioCruces Health Research Institute, Barakaldo, Bizkaia, Spain
| | - Rosa Guarch
- Department of Pathology, Complejo Hospitalario B de Navarra, Pamplona, Navarra, Spain
| | - Jesús M Cortés
- Quantitative Biomedicine Unit, BioCruces Health Research Institute, Barakaldo, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia, Spain.,Department of Cell Biology and Histology, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain
| | - Rafael Pulido
- Biomarkers in Cancer Unit, BioCruces Health Research Institute, Barakaldo, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - Roberto Llarena
- Department of Urology, Cruces University Hospital, University of the Basque Country (UPV/EHU), Barakaldo, Bizkaia, Spain
| | - Javier C Angulo
- Department of Urology, Hospital de Getafe, Universidad Europea de Madrid, Madrid, Spain
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21
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Mingo J, Erramuzpe A, Luna S, Aurtenetxe O, Amo L, Diez I, Schepens JTG, Hendriks WJAJ, Cortés JM, Pulido R. One-Tube-Only Standardized Site-Directed Mutagenesis: An Alternative Approach to Generate Amino Acid Substitution Collections. PLoS One 2016; 11:e0160972. [PMID: 27548698 PMCID: PMC4993582 DOI: 10.1371/journal.pone.0160972] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 05/23/2016] [Accepted: 07/27/2016] [Indexed: 12/30/2022] Open
Abstract
Site-directed mutagenesis (SDM) is a powerful tool to create defined collections of protein variants for experimental and clinical purposes, but effectiveness is compromised when a large number of mutations is required. We present here a one-tube-only standardized SDM approach that generates comprehensive collections of amino acid substitution variants, including scanning- and single site-multiple mutations. The approach combines unified mutagenic primer design with the mixing of multiple distinct primer pairs and/or plasmid templates to increase the yield of a single inverse-PCR mutagenesis reaction. Also, a user-friendly program for automatic design of standardized primers for Ala-scanning mutagenesis is made available. Experimental results were compared with a modeling approach together with stochastic simulation data. For single site-multiple mutagenesis purposes and for simultaneous mutagenesis in different plasmid backgrounds, combination of primer sets and/or plasmid templates in a single reaction tube yielded the distinct mutations in a stochastic fashion. For scanning mutagenesis, we found that a combination of overlapping primer sets in a single PCR reaction allowed the yield of different individual mutations, although this yield did not necessarily follow a stochastic trend. Double mutants were generated when the overlap of primer pairs was below 60%. Our results illustrate that one-tube-only SDM effectively reduces the number of reactions required in large-scale mutagenesis strategies, facilitating the generation of comprehensive collections of protein variants suitable for functional analysis.
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Affiliation(s)
- Janire Mingo
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, Barakaldo, Spain
| | - Asier Erramuzpe
- Quantitative Biomedicine Unit, Biocruces Health Research Institute, Barakaldo, Spain
| | - Sandra Luna
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, Barakaldo, Spain
| | - Olaia Aurtenetxe
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, Barakaldo, Spain
| | - Laura Amo
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, Barakaldo, Spain
| | - Ibai Diez
- Quantitative Biomedicine Unit, Biocruces Health Research Institute, Barakaldo, Spain
| | - Jan T. G. Schepens
- Department of Cell Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Wiljan J. A. J. Hendriks
- Department of Cell Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Jesús M. Cortés
- Quantitative Biomedicine Unit, Biocruces Health Research Institute, Barakaldo, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, Barakaldo, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- * E-mail: ;
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22
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Ortega-Martínez I, Gardeazabal J, Erramuzpe A, Sanchez-Diez A, Cortés J, García-Vázquez MD, Pérez-Yarza G, Izu R, Luís Díaz-Ramón J, de la Fuente IM, Asumendi A, Boyano MD. Vitronectin and dermcidin serum levels predict the metastatic progression of AJCC I-II early-stage melanoma. Int J Cancer 2016; 139:1598-607. [PMID: 27216146 PMCID: PMC5089559 DOI: 10.1002/ijc.30202] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [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: 01/03/2016] [Accepted: 05/11/2016] [Indexed: 01/03/2023]
Abstract
Like many cancers, an early diagnosis of melanoma is fundamental to ensure a good prognosis, although an important proportion of stage I-II patients may still develop metastasis during follow-up. The aim of this work was to discover serum biomarkers in patients diagnosed with primary melanoma that identify those at a high risk of developing metastasis during the follow-up period. Proteomic and mass spectrophotometry analysis was performed on serum obtained from patients who developed metastasis during the first years after surgery for primary tumors and compared with that from patients who remained disease-free for more than 10 years after surgery. Five proteins were selected for validation as prognostic factors in 348 melanoma patients and 100 controls by ELISA: serum amyloid A and clusterin; immune system proteins; the cell adhesion molecules plakoglobin and vitronectin and the antimicrobial protein dermcidin. Compared to healthy controls, melanoma patients have high serum levels of these proteins at the moment of melanoma diagnosis, although the specific values were not related to the histopathological stage of the tumors. However, an analysis based on classification together with multivariate statistics showed that tumor stage, vitronectin and dermcidin levels were associated with the metastatic progression of patients with early-stage melanoma. Although melanoma patients have increased serum dermcidin levels, the REPTree classifier showed that levels of dermcidin <2.98 μg/ml predict metastasis in AJCC stage II patients. These data suggest that vitronectin and dermcidin are potent biomarkers of prognosis, which may help to improve the personalized medical care of melanoma patients and their survival.
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Affiliation(s)
- Idoia Ortega-Martínez
- Department of Cell Biology and Histology, Faculty of Medicine and Dentistry, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain
| | - Jesús Gardeazabal
- Department of Dermatology, Ophthalmology and Otorhinolaryngology, Faculty of Medicine and Dentistry, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain.,BioCruces Health Research Institute, Plaza De Cruces S/N, Barakaldo, Bizkaia, Spain
| | - Asier Erramuzpe
- BioCruces Health Research Institute, Plaza De Cruces S/N, Barakaldo, Bizkaia, Spain
| | - Ana Sanchez-Diez
- Department of Dermatology, Ophthalmology and Otorhinolaryngology, Faculty of Medicine and Dentistry, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain.,BioCruces Health Research Institute, Plaza De Cruces S/N, Barakaldo, Bizkaia, Spain
| | - Jesús Cortés
- Department of Cell Biology and Histology, Faculty of Medicine and Dentistry, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain.,BioCruces Health Research Institute, Plaza De Cruces S/N, Barakaldo, Bizkaia, Spain.,Ikerbasque: The Basque Foundation for Science, Bilbao, Spain
| | - María D García-Vázquez
- Department of Cell Biology and Histology, Faculty of Medicine and Dentistry, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain
| | - Gorka Pérez-Yarza
- Department of Cell Biology and Histology, Faculty of Medicine and Dentistry, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain.,BioCruces Health Research Institute, Plaza De Cruces S/N, Barakaldo, Bizkaia, Spain
| | - Rosa Izu
- Department of Dermatology, Ophthalmology and Otorhinolaryngology, Faculty of Medicine and Dentistry, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain.,BioCruces Health Research Institute, Plaza De Cruces S/N, Barakaldo, Bizkaia, Spain
| | - Jose Luís Díaz-Ramón
- Department of Dermatology, Ophthalmology and Otorhinolaryngology, Faculty of Medicine and Dentistry, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain.,BioCruces Health Research Institute, Plaza De Cruces S/N, Barakaldo, Bizkaia, Spain
| | - Ildefonso M de la Fuente
- Institute of Parasitology and Biomedicine Lopez-Neyra, Parque Tecnológico Ciencias De La Salud, Avenida Del Conocimiento S/N, Armilla, Granada, Spain
| | - Aintzane Asumendi
- Department of Cell Biology and Histology, Faculty of Medicine and Dentistry, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain.,BioCruces Health Research Institute, Plaza De Cruces S/N, Barakaldo, Bizkaia, Spain
| | - María D Boyano
- Department of Cell Biology and Histology, Faculty of Medicine and Dentistry, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain.,BioCruces Health Research Institute, Plaza De Cruces S/N, Barakaldo, Bizkaia, Spain
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23
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Zaldumbide L, Erramuzpe A, Guarch R, Pulido R, Cortés JM, López JI. Snail heterogeneity in clear cell renal cell carcinoma. BMC Cancer 2016; 16:194. [PMID: 26951092 PMCID: PMC4782341 DOI: 10.1186/s12885-016-2237-x] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 03/01/2016] [Indexed: 12/17/2022] Open
Abstract
Background Intratumor heterogeneity may be responsible of the unpredictable aggressive clinical behavior that some clear cell renal cell carcinomas display. This clinical uncertainty may be caused by insufficient sampling, leaving out of histological analysis foci of high grade tumor areas. Although molecular approaches are providing important information on renal intratumor heterogeneity, a focus on this topic from the practicing pathologist’ perspective is still pending. Methods Four distant tumor areas of 40 organ-confined clear cell renal cell carcinomas were selected for histopathological and immunohistochemical evaluation. Tumor size, cell type (clear/granular), Fuhrman’s grade, Staging, as well as immunostaining with Snail, ZEB1, Twist, Vimentin, E-cadherin, β-catenin, PTEN, p-Akt, p110α, and SETD2, were analyzed for intratumor heterogeneity using a classification and regression tree algorithm. Results Cell type and Fuhrman’s grade were heterogeneous in 12.5 and 60 % of the tumors, respectively. If cell type was homogeneous (clear cell) then the tumors were low-grade in 88.57 % of cases. Immunostaining heterogeneity was significant in the series and oscillated between 15 % for p110α and 80 % for Snail. When Snail immunostaining was homogeneous the tumor was histologically homogeneous in 100 % of cases. If Snail was heterogeneous, the tumor was heterogeneous in 75 % of the cases. Average tumor diameter was 4.3 cm. Tumors larger than 3.7 cm were heterogeneous for Vimentin immunostaining in 72.5 % of cases. Tumors displaying negative immunostaining for both ZEB1 and Twist were low grade in 100 % of the cases. Conclusions Intratumor heterogeneity is a common event in clear cell renal cell carcinoma, which can be monitored by immunohistochemistry in routine practice. Snail seems to be particularly useful in the identification of intratumor heterogeneity. The suitability of current sampling protocols in renal cancer is discussed.
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Affiliation(s)
- Laura Zaldumbide
- Department of Pathology, Cruces University Hospital, University of the Basque Country (UPV/EHU), Plaza de Cruces s/n, 48903, Barakaldo, Bizkaia, Spain.
| | - Asier Erramuzpe
- Quantitative Biomedicine Unit, Biocruces Health Research Institute, Barakaldo, Bizkaia, Spain.
| | - Rosa Guarch
- Department of Pathology, Complejo Hospitalario de Navarra-Hospital Virgen del Camino, Pamplona, Navarra, Spain.
| | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Health Research Institute, Barakaldo, Bizkaia, Spain. .,Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia, Spain.
| | - Jesús M Cortés
- Quantitative Biomedicine Unit, Biocruces Health Research Institute, Barakaldo, Bizkaia, Spain. .,Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia, Spain. .,Department of Cell Biology and Histology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain.
| | - José I López
- Department of Pathology, Cruces University Hospital, University of the Basque Country (UPV/EHU), Plaza de Cruces s/n, 48903, Barakaldo, Bizkaia, Spain. .,Biomarkers in Cancer Unit, Biocruces Health Research Institute, Barakaldo, Bizkaia, Spain.
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Erramuzpe A, Ortega GJ, Pastor J, Sola RGD, Marinazzo D, Stramaglia S, Cortes JM. Identification of redundant and synergetic circuits in triplets of electrophysiological data. J Neural Eng 2015; 12:066007. [DOI: 10.1088/1741-2560/12/6/066007] [Citation(s) in RCA: 13] [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] [Indexed: 11/11/2022]
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25
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Diez I, Erramuzpe A, Escudero I, Mateos B, Cabrera A, Marinazzo D, Sanz-Arigita EJ, Stramaglia S, Cortes Diaz JM. Information Flow Between Resting-State Networks. Brain Connect 2015; 5:554-64. [PMID: 26177254 DOI: 10.1089/brain.2014.0337] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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: 12/23/2022] Open
Abstract
UNLABELLED The resting brain dynamics self-organize into a finite number of correlated patterns known as resting-state networks (RSNs). It is well known that techniques such as independent component analysis can separate the brain activity at rest to provide such RSNs, but the specific pattern of interaction between RSNs is not yet fully understood. To this aim, we propose here a novel method to compute the information flow (IF) between different RSNs from resting-state magnetic resonance imaging. After hemodynamic response function blind deconvolution of all voxel signals, and under the hypothesis that RSNs define regions of interest, our method first uses principal component analysis to reduce dimensionality in each RSN to next compute IF (estimated here in terms of transfer entropy) between the different RSNs by systematically increasing k (the number of principal components used in the calculation). When k=1, this method is equivalent to computing IF using the average of all voxel activities in each RSN. For k≥1, our method calculates the k multivariate IF between the different RSNs. We find that the average IF among RSNs is dimension dependent, increasing from k=1 (i.e., the average voxel activity) up to a maximum occurring at k=5 and to finally decay to zero for k≥10. This suggests that a small number of components (close to five) is sufficient to describe the IF pattern between RSNs. Our method--addressing differences in IF between RSNs for any generic data--can be used for group comparison in health or disease. To illustrate this, we have calculated the inter-RSN IF in a data set of Alzheimer's disease (AD) to find that the most significant differences between AD and controls occurred for k=2, in addition to AD showing increased IF w.r.t. CONTROLS The spatial localization of the k=2 component, within RSNs, allows the characterization of IF differences between AD and controls.
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Affiliation(s)
- Ibai Diez
- 1 Computational Neuroimaging Lab, Biocruces Health Research Institute, Cruces University Hospital , Barakaldo, Spain
| | - Asier Erramuzpe
- 1 Computational Neuroimaging Lab, Biocruces Health Research Institute, Cruces University Hospital , Barakaldo, Spain
| | - Iñaki Escudero
- 1 Computational Neuroimaging Lab, Biocruces Health Research Institute, Cruces University Hospital , Barakaldo, Spain .,2 Radiology Service, Cruces University Hospital , Barakaldo, Spain
| | - Beatriz Mateos
- 1 Computational Neuroimaging Lab, Biocruces Health Research Institute, Cruces University Hospital , Barakaldo, Spain .,2 Radiology Service, Cruces University Hospital , Barakaldo, Spain
| | | | - Daniele Marinazzo
- 4 Department of Data Analysis, Faculty of Psychology and Educational Sciences, Ghent University , Gent, Belgium
| | | | - Sebastiano Stramaglia
- 6 Dipartimento di Fisica, Universita degli Studi di Bari and INFN , Bari, Italy .,7 BCAM-Basque Center for Applied Mathematics , Bilbao, Spain
| | - Jesus M Cortes Diaz
- 1 Computational Neuroimaging Lab, Biocruces Health Research Institute, Cruces University Hospital , Barakaldo, Spain .,8 Ikerbasque, The Basque Foundation for Science , Bilbao, Spain .,9 Departamento de Biologia Celular e Histologia, University of the Basque Country , Leioa, Spain
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Erramuzpe A, Encinas JM, Sierra A, Maletic-Savatic M, Brewster AL, Anderson AE, Stramaglia S, Cortes JM. Longitudinal variations of brain functional connectivity: A case report study based on a mouse model of epilepsy. F1000Res 2015; 4:144. [PMID: 26167275 PMCID: PMC4482210 DOI: 10.12688/f1000research.6570.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/15/2015] [Indexed: 11/20/2022] Open
Abstract
Brain Functional Connectivity (FC) quantifies statistical dependencies between areas of the brain. FC has been widely used to address altered function of brain circuits in control conditions compared to different pathological states, including epilepsy, a major neurological disorder. However, FC also has the as yet unexplored potential to help us understand the pathological transformation of the brain circuitry. Our hypothesis is that FC can differentiate global brain interactions across a time-scale of days. To this end, we present a case report study based on a mouse model for epilepsy and analyze longitudinal intracranial electroencephalography data of epilepsy to calculate FC changes from the initial insult (status epilepticus) and over the latent period, when epileptogenic networks emerge, and at chronic epilepsy, when unprovoked seizures occur as spontaneous events. We found that the overall network FC at low frequency bands decreased immediately after status epilepticus was provoked, and increased monotonously later on during the latent period. Overall, our results demonstrate the capacity of FC to address longitudinal variations of brain connectivity across the establishment of pathological states.
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Affiliation(s)
- A Erramuzpe
- Biocruces Health Research Institute, Cruces University Hospital, Barakaldo, 48903, Spain
| | - J M Encinas
- Achucarro Basque Center for Neuroscience, Zamudio, 48170, Spain.,University of the Basque Country (UPV/EHU), Leioa, 48940, Spain.,Ikerbasque: The Basque Foundation for Science, Bilbao, 48013, Spain
| | - A Sierra
- Achucarro Basque Center for Neuroscience, Zamudio, 48170, Spain.,University of the Basque Country (UPV/EHU), Leioa, 48940, Spain.,Ikerbasque: The Basque Foundation for Science, Bilbao, 48013, Spain
| | - M Maletic-Savatic
- Neurological Research Institute, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - A L Brewster
- Neurological Research Institute, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Anne E Anderson
- Neurological Research Institute, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - S Stramaglia
- Dipartimento di Fisica, Universita degla Studi di Bari and INFN, Bari, 70125, Italy.,BCAM, Basque Center for Applied Mathematics, Bilbao, 48009, Spain
| | - Jesus M Cortes
- Biocruces Health Research Institute, Cruces University Hospital, Barakaldo, 48903, Spain.,University of the Basque Country (UPV/EHU), Leioa, 48940, Spain.,Ikerbasque: The Basque Foundation for Science, Bilbao, 48013, Spain
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Zaldumbide L, Erramuzpe A, Guarch R, Cortés JM, López JI. Large (>3.8 cm) clear cell renal cell carcinomas are morphologically and immunohistochemically heterogeneous. Virchows Arch 2014; 466:61-6. [DOI: 10.1007/s00428-014-1673-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 09/10/2014] [Accepted: 10/13/2014] [Indexed: 12/21/2022]
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