1
|
Piluso S, Souedet N, Jan C, Hérard AS, Clouchoux C, Delzescaux T. giRAff: an automated atlas segmentation tool adapted to single histological slices. Front Neurosci 2024; 17:1230814. [PMID: 38274499 PMCID: PMC10808556 DOI: 10.3389/fnins.2023.1230814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 10/31/2023] [Indexed: 01/27/2024] Open
Abstract
Conventional histology of the brain remains the gold standard in the analysis of animal models. In most biological studies, standard protocols usually involve producing a limited number of histological slices to be analyzed. These slices are often selected into a specific anatomical region of interest or around a specific pathological lesion. Due to the lack of automated solutions to analyze such single slices, neurobiologists perform the segmentation of anatomical regions manually most of the time. Because the task is long, tedious, and operator-dependent, we propose an automated atlas segmentation method called giRAff, which combines rigid and affine registrations and is suitable for conventional histological protocols involving any number of single slices from a given mouse brain. In particular, the method has been tested on several routine experimental protocols involving different anatomical regions of different sizes and for several brains. For a given set of single slices, the method can automatically identify the corresponding slices in the mouse Allen atlas template with good accuracy and segmentations comparable to those of an expert. This versatile and generic method allows the segmentation of any single slice without additional anatomical context in about 1 min. Basically, our proposed giRAff method is an easy-to-use, rapid, and automated atlas segmentation tool compliant with a wide variety of standard histological protocols.
Collapse
Affiliation(s)
- Sébastien Piluso
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
- WITSEE, Paris, France
| | - Nicolas Souedet
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
| | - Caroline Jan
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
| | - Anne-Sophie Hérard
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
| | | | - Thierry Delzescaux
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
| |
Collapse
|
2
|
I F. The unique neuropathological vulnerability of the human brain to aging. Ageing Res Rev 2023; 87:101916. [PMID: 36990284 DOI: 10.1016/j.arr.2023.101916] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/19/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023]
Abstract
Alzheimer's disease (AD)-related neurofibrillary tangles (NFT), argyrophilic grain disease (AGD), aging-related tau astrogliopathy (ARTAG), limbic predominant TDP-43 proteinopathy (LATE), and amygdala-predominant Lewy body disease (LBD) are proteinopathies that, together with hippocampal sclerosis, progressively appear in the elderly affecting from 50% to 99% of individuals aged 80 years, depending on the disease. These disorders usually converge on the same subject and associate with additive cognitive impairment. Abnormal Tau, TDP-43, and α-synuclein pathologies progress following a pattern consistent with an active cell-to-cell transmission and abnormal protein processing in the host cell. However, cell vulnerability and transmission pathways are specific for each disorder, albeit abnormal proteins may co-localize in particular neurons. All these alterations are unique or highly prevalent in humans. They all affect, at first, the archicortex and paleocortex to extend at later stages to the neocortex and other regions of the telencephalon. These observations show that the phylogenetically oldest areas of the human cerebral cortex and amygdala are not designed to cope with the lifespan of actual humans. New strategies aimed at reducing the functional overload of the human telencephalon, including optimization of dream repair mechanisms and implementation of artificial circuit devices to surrogate specific brain functions, appear promising.
Collapse
Affiliation(s)
- Ferrer I
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain; Emeritus Researcher of the Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain; Biomedical Research Network of Neurodegenerative Diseases (CIBERNED), Barcelona, Spain; Institute of Neurosciences, University of Barcelona, Barcelona, Spain; Hospitalet de Llobregat, Barcelona, Spain.
| |
Collapse
|
3
|
Li X, Ospitalieri S, Robberechts T, Hofmann L, Schmid C, Rijal Upadhaya A, Koper MJ, von Arnim CAF, Kumar S, Willem M, Gnoth K, Ramakers M, Schymkowitz J, Rousseau F, Walter J, Ronisz A, Balakrishnan K, Thal DR. Seeding, maturation and propagation of amyloid β-peptide aggregates in Alzheimer’s disease. Brain 2022; 145:3558-3570. [PMID: 36270003 DOI: 10.1093/brain/awac202] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Alzheimer’s disease is neuropathologically characterized by the deposition of the amyloid β-peptide (Aβ) as amyloid plaques. Aβ plaque pathology starts in the neocortex before it propagates into further brain regions. Moreover, Aβ aggregates undergo maturation indicated by the occurrence of post-translational modifications. Here, we show that propagation of Aβ plaques is led by presumably non-modified Aβ followed by Aβ aggregate maturation. This sequence was seen neuropathologically in human brains and in amyloid precursor protein transgenic mice receiving intracerebral injections of human brain homogenates from cases varying in Aβ phase, Aβ load and Aβ maturation stage. The speed of propagation after seeding in mice was best related to the Aβ phase of the donor, the progression speed of maturation to the stage of Aβ aggregate maturation. Thus, different forms of Aβ can trigger propagation/maturation of Aβ aggregates, which may explain the lack of success when therapeutically targeting only specific forms of Aβ.
Collapse
Affiliation(s)
- Xiaohang Li
- Department of Imaging and Pathology, Laboratory of Neuropathology, Leuven Brain Institute, KU-Leuven , Leuven , Belgium
| | - Simona Ospitalieri
- Department of Imaging and Pathology, Laboratory of Neuropathology, Leuven Brain Institute, KU-Leuven , Leuven , Belgium
| | - Tessa Robberechts
- Department of Imaging and Pathology, Laboratory of Neuropathology, Leuven Brain Institute, KU-Leuven , Leuven , Belgium
| | - Linda Hofmann
- Institute of Pathology, Laboratory of Neuropathology, Ulm University , Ulm , Germany
| | - Christina Schmid
- Institute of Pathology, Laboratory of Neuropathology, Ulm University , Ulm , Germany
| | - Ajeet Rijal Upadhaya
- Institute of Pathology, Laboratory of Neuropathology, Ulm University , Ulm , Germany
| | - Marta J Koper
- Department of Imaging and Pathology, Laboratory of Neuropathology, Leuven Brain Institute, KU-Leuven , Leuven , Belgium
- Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, KU-Leuven (University of Leuven), Leuven Brain Institute , Leuven , Belgium
- Center for Brain and Disease Research, VIB , Leuven , Belgium
| | - Christine A F von Arnim
- Department of Neurology, Ulm University , Ulm , Germany
- Division of Geriatrics, University Medical Center Göttingen , Göttingen , Germany
| | - Sathish Kumar
- Department of Neurology, University of Bonn , Bonn , Germany
| | - Michael Willem
- Chair of Metabolic Biochemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich , Munich , Germany
| | - Kathrin Gnoth
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology , Halle , Germany
| | - Meine Ramakers
- Center for Brain and Disease Research, VIB , Leuven , Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU-Leuven , Leuven , Belgium
| | - Joost Schymkowitz
- Center for Brain and Disease Research, VIB , Leuven , Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU-Leuven , Leuven , Belgium
| | - Frederic Rousseau
- Center for Brain and Disease Research, VIB , Leuven , Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU-Leuven , Leuven , Belgium
| | - Jochen Walter
- Department of Neurology, University of Bonn , Bonn , Germany
| | - Alicja Ronisz
- Department of Imaging and Pathology, Laboratory of Neuropathology, Leuven Brain Institute, KU-Leuven , Leuven , Belgium
| | - Karthikeyan Balakrishnan
- Institute of Pathology, Laboratory of Neuropathology, Ulm University , Ulm , Germany
- Department of Gene Therapy, Ulm University , Ulm , Germany
| | - Dietmar Rudolf Thal
- Department of Imaging and Pathology, Laboratory of Neuropathology, Leuven Brain Institute, KU-Leuven , Leuven , Belgium
- Institute of Pathology, Laboratory of Neuropathology, Ulm University , Ulm , Germany
- Department of Pathology, UZ-Leuven , Leuven , Belgium
| |
Collapse
|
4
|
Baerends E, Soud K, Folke J, Pedersen AK, Henmar S, Konrad L, Lycas MD, Mori Y, Pakkenberg B, Woldbye DPD, Dmytriyeva O, Pankratova S. Modeling the early stages of Alzheimer's disease by administering intracerebroventricular injections of human native Aβ oligomers to rats. Acta Neuropathol Commun 2022; 10:113. [PMID: 35974377 PMCID: PMC9380371 DOI: 10.1186/s40478-022-01417-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 07/29/2022] [Indexed: 11/10/2022] Open
Abstract
Alzheimer's disease (AD) is a progressive and irreversible neurodegenerative disease characterized by the accumulation of aggregated amyloid beta (Aβ) and hyperphosphorylated tau along with a slow decline in cognitive functions. Unlike advanced AD, the initial steps of AD pathophysiology have been poorly investigated, partially due to limited availability of animal models focused on the early, plaque-free stages of the disease. The aim of this study was to evaluate the early behavioral, anatomical and molecular alterations in wild-type rats following intracerebroventricular injections of human Aβ oligomers (AβOs). Bioactive human AD and nondemented control brain tissue extracts were characterized using ELISA and proteomics approaches. Following a bilateral infusion, rats underwent behavioral testing, including the elevated plus maze, social recognition test, Morris water maze and Y-maze within 6 weeks postinjection. An analysis of brain structure was performed with manganese-enhanced MRI. Collected brain tissues were analyzed using stereology, immunohistochemistry, ELISA and qPCR. No sensorimotor deficits affecting motor performance on different maze tasks were observed, nor was spatial memory disturbed in AD rats. In contrast, a significant impairment of social memory became evident at 21 days postinjection. This deficit was associated with a significantly decreased volume of the lateral entorhinal cortex and a tendency toward a decrease in the total brain volume. Significant increase of cleaved caspase-3-positive cells, microglial activation and proinflammatory responses accompanied by altered expression of synaptic markers were observed in the hippocampus of AD rats with immunohistochemical and qPCR approaches at 6 weeks postinjection. Our data suggest that the social memory impairment observed in AβO-injected rats might be determined by neuroinflammatory responses and synaptopathy. An infusion of native oligomeric Aβ in the rat brain represents a feasible tool to model early plaque-free events associated with AD.
Collapse
Affiliation(s)
- Eva Baerends
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Katia Soud
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Jonas Folke
- Centre for Neuroscience and Stereology, Department of Neurology,, Bispebjerg-Frederiksberg Hospital, Copenhagen University Hospital, Copenhagen, Denmark.,Copenhagen Center for Translational Research, Bispebjerg-Frederiksberg Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anna-Kathrine Pedersen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Simon Henmar
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Lisa Konrad
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Matthew D Lycas
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Yuki Mori
- Center for Translational Neuromedicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bente Pakkenberg
- Centre for Neuroscience and Stereology, Department of Neurology,, Bispebjerg-Frederiksberg Hospital, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David P D Woldbye
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Oksana Dmytriyeva
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stanislava Pankratova
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark. .,Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
5
|
Willbold D, Strodel B, Schröder GF, Hoyer W, Heise H. Amyloid-type Protein Aggregation and Prion-like Properties of Amyloids. Chem Rev 2021; 121:8285-8307. [PMID: 34137605 DOI: 10.1021/acs.chemrev.1c00196] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review will focus on the process of amyloid-type protein aggregation. Amyloid fibrils are an important hallmark of protein misfolding diseases and therefore have been investigated for decades. Only recently, however, atomic or near-atomic resolution structures have been elucidated from various in vitro and ex vivo obtained fibrils. In parallel, the process of fibril formation has been studied in vitro under highly artificial but comparatively reproducible conditions. The review starts with a summary of what is known and speculated from artificial in vitro amyloid-type protein aggregation experiments. A partially hypothetic fibril selection model will be described that may be suitable to explain why amyloid fibrils look the way they do, in particular, why at least all so far reported high resolution cryo-electron microscopy obtained fibril structures are in register, parallel, cross-β-sheet fibrils that mostly consist of two protofilaments twisted around each other. An intrinsic feature of the model is the prion-like nature of all amyloid assemblies. Transferring the model from the in vitro point of view to the in vivo situation is not straightforward, highly hypothetic, and leaves many open questions that need to be addressed in the future.
Collapse
Affiliation(s)
- Dieter Willbold
- Institute of Biological Information Processing, Structural Biochemistry, IBI-7, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.,Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (State University), 141700 Dolgoprudny, Russia
| | - Birgit Strodel
- Institute of Biological Information Processing, Structural Biochemistry, IBI-7, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institute of Theoretical and Computational Chemistry, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Gunnar F Schröder
- Institute of Biological Information Processing, Structural Biochemistry, IBI-7, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Physics Department, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Henrike Heise
- Institute of Biological Information Processing, Structural Biochemistry, IBI-7, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| |
Collapse
|