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Otomo K, Omura T, Nozawa Y, Edwards SJ, Sato Y, Saito Y, Yagishita S, Uchida H, Watakabe Y, Naitou K, Yanai R, Sahara N, Takagi S, Katayama R, Iwata Y, Shiokawa T, Hayakawa Y, Otsuka K, Watanabe-Takano H, Haneda Y, Fukuhara S, Fujiwara M, Nii T, Meno C, Takeshita N, Yashiro K, Rosales Rocabado JM, Kaku M, Yamada T, Oishi Y, Koike H, Cheng Y, Sekine K, Koga JI, Sugiyama K, Kimura K, Karube F, Kim H, Manabe I, Nemoto T, Tainaka K, Hamada A, Brismar H, Susaki EA. descSPIM: an affordable and easy-to-build light-sheet microscope optimized for tissue clearing techniques. Nat Commun 2024; 15:4941. [PMID: 38866781 PMCID: PMC11169475 DOI: 10.1038/s41467-024-49131-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/24/2024] [Indexed: 06/14/2024] Open
Abstract
Despite widespread adoption of tissue clearing techniques in recent years, poor access to suitable light-sheet fluorescence microscopes remains a major obstacle for biomedical end-users. Here, we present descSPIM (desktop-equipped SPIM for cleared specimens), a low-cost ($20,000-50,000), low-expertise (one-day installation by a non-expert), yet practical do-it-yourself light-sheet microscope as a solution for this bottleneck. Even the most fundamental configuration of descSPIM enables multi-color imaging of whole mouse brains and a cancer cell line-derived xenograft tumor mass for the visualization of neurocircuitry, assessment of drug distribution, and pathological examination by false-colored hematoxylin and eosin staining in a three-dimensional manner. Academically open-sourced ( https://github.com/dbsb-juntendo/descSPIM ), descSPIM allows routine three-dimensional imaging of cleared samples in minutes. Thus, the dissemination of descSPIM will accelerate biomedical discoveries driven by tissue clearing technologies.
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Affiliation(s)
- Kohei Otomo
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Biochemistry II, Juntendo University School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Takaki Omura
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Neurosurgery, University of Tokyo, Tokyo, Japan
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuki Nozawa
- Biochemistry II, Juntendo University School of Medicine, Tokyo, Japan
| | - Steven J Edwards
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Yukihiko Sato
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yuri Saito
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shigehiro Yagishita
- Department of Pharmacology and Therapeutics, Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Tokyo, Japan
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo, Japan
| | - Hitoshi Uchida
- Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yuki Watakabe
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Kiyotada Naitou
- Department of Basic Veterinary Science, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Rin Yanai
- Advanced Neuroimaging Center, Institute for Quantum Medical Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Naruhiko Sahara
- Advanced Neuroimaging Center, Institute for Quantum Medical Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Satoshi Takagi
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ryohei Katayama
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yusuke Iwata
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshiro Shiokawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoku Hayakawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kensuke Otsuka
- Biology and Environmental Chemistry Division, Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry, Chiba, Japan
| | - Haruko Watanabe-Takano
- Department of Molecular Pathophysiology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Yuka Haneda
- Department of Molecular Pathophysiology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Shigetomo Fukuhara
- Department of Molecular Pathophysiology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Miku Fujiwara
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takenobu Nii
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Chikara Meno
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naoki Takeshita
- Anatomy and Developmental Biology, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kenta Yashiro
- Anatomy and Developmental Biology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Juan Marcelo Rosales Rocabado
- Division of Bio-prosthodontics, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Masaru Kaku
- Division of Bio-prosthodontics, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Tatsuya Yamada
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
| | - Yumiko Oishi
- Department of Meidical Biochemistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroyuki Koike
- Department of Meidical Biochemistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yinglan Cheng
- Department of Meidical Biochemistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Keisuke Sekine
- Laboratory of Cancer Cell Systems, National Cancer Center Research Institute, Tokyo, Japan
| | - Jun-Ichiro Koga
- The Second Department of Internal Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Kaori Sugiyama
- Institute for Advanced Research of Biosystem Dynamics, Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Kenichi Kimura
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan
| | - Fuyuki Karube
- Lab of Histology and Cytology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Hyeree Kim
- Department of Systems Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ichiro Manabe
- Department of Systems Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomomi Nemoto
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Kazuki Tainaka
- Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akinobu Hamada
- Department of Pharmacology and Therapeutics, Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Tokyo, Japan
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo, Japan
| | - Hjalmar Brismar
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Etsuo A Susaki
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan.
- Biochemistry II, Juntendo University School of Medicine, Tokyo, Japan.
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan.
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Oz S, Saar G, Olszakier S, Heinrich R, Kompanets MO, Berlin S. Revealing the MRI-Contrast in Optically Cleared Brains. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400316. [PMID: 38647385 PMCID: PMC11165557 DOI: 10.1002/advs.202400316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/10/2024] [Indexed: 04/25/2024]
Abstract
The current consensus holds that optically-cleared specimens are unsuitable for Magnetic Resonance Imaging (MRI); exhibiting absence of contrast. Prior studies combined MRI with tissue-clearing techniques relying on the latter's ability to eliminate lipids, thereby fostering the assumption that lipids constitute the primary source of ex vivo MRI-contrast. Nevertheless, these findings contradict an extensive body of literature that underscores the contribution of other features to contrast. Furthermore, it remains unknown whether non-delipidating clearing methods can produce MRI-compatible specimens or whether MRI-contrast can be re-established. These limitations hinder the development of multimodal MRI-light-microscopy (LM) imaging approaches. This study assesses the relation between MRI-contrast, and delipidation in optically-cleared whole brains following different tissue-clearing approaches. It is demonstrated that uDISCO and ECi-brains are MRI-compatible upon tissue rehydration, despite both methods' substantial delipidating-nature. It is also demonstrated that, whereas Scale-clearing preserves most lipids, Scale-cleared brain lack MRI-contrast. Furthermore, MRI-contrast is restored to lipid-free CLARITY-brains without introducing lipids. Our results thereby dissociate between the essentiality of lipids to MRI-contrast. A tight association is found between tissue expansion, hyperhydration and loss of MRI-contrast. These findings then enabled us to develop a multimodal MRI-LM-imaging approach, opening new avenues to bridge between the micro- and mesoscale for biomedical research and clinical applications.
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Affiliation(s)
- Shimrit Oz
- Department of NeuroscienceFaculty of MedicineTechnion‐Israel Institute of TechnologyHaifa3525433Israel
| | - Galit Saar
- Biomedical Core FacilityFaculty of MedicineTechnion‐Israel Institute of TechnologyHaifa3525433Israel
| | - Shunit Olszakier
- Department of NeuroscienceFaculty of MedicineTechnion‐Israel Institute of TechnologyHaifa3525433Israel
| | - Ronit Heinrich
- Department of NeuroscienceFaculty of MedicineTechnion‐Israel Institute of TechnologyHaifa3525433Israel
| | - Mykhail O. Kompanets
- L.M. Litvinenko Institute of Physico‐Organic Chemistry and Coal ChemistryNational Academy of Sciences of UkraineKyivUkraine
| | - Shai Berlin
- Department of NeuroscienceFaculty of MedicineTechnion‐Israel Institute of TechnologyHaifa3525433Israel
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Mansour H, Azrak R, Cook JJ, Hornburg KJ, Qi Y, Tian Y, Williams RW, Yeh FC, White LE, Johnson GA. An Open Resource: MR and light sheet microscopy stereotaxic atlas of the mouse brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587246. [PMID: 38586051 PMCID: PMC10996689 DOI: 10.1101/2024.03.28.587246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
We have combined MR histology and light sheet microscopy (LSM) of five postmortem C57BL/6J mouse brains in a stereotaxic space based on micro-CT yielding a multimodal 3D atlas with the highest spatial and contrast resolution yet reported. Brains were imaged in situ with multi gradient echo (mGRE) and diffusion tensor imaging (DTI) at 15 μm resolution (∼ 2.4 million times that of clinical MRI). Scalar images derived from the average DTI and mGRE provide unprecedented contrast in 14 complementary 3D volumes, each highlighting distinct histologic features. The same tissues scanned with LSM and registered into the stereotaxic space provide 17 different molecular cell type stains. The common coordinate framework labels (CCFv3) complete the multimodal atlas. The atlas has been used to correct distortions in the Allen Brain Atlas and harmonize it with Franklin Paxinos. It provides a unique resource for stereotaxic labeling of mouse brain images from many sources.
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Pan MT, Zhang H, Li XJ, Guo XY. Genetically modified non-human primate models for research on neurodegenerative diseases. Zool Res 2024; 45:263-274. [PMID: 38287907 PMCID: PMC11017080 DOI: 10.24272/j.issn.2095-8137.2023.197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 01/25/2024] [Indexed: 01/31/2024] Open
Abstract
Neurodegenerative diseases (NDs) are a group of debilitating neurological disorders that primarily affect elderly populations and include Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS). Currently, there are no therapies available that can delay, stop, or reverse the pathological progression of NDs in clinical settings. As the population ages, NDs are imposing a huge burden on public health systems and affected families. Animal models are important tools for preclinical investigations to understand disease pathogenesis and test potential treatments. While numerous rodent models of NDs have been developed to enhance our understanding of disease mechanisms, the limited success of translating findings from animal models to clinical practice suggests that there is still a need to bridge this translation gap. Old World non-human primates (NHPs), such as rhesus, cynomolgus, and vervet monkeys, are phylogenetically, physiologically, biochemically, and behaviorally most relevant to humans. This is particularly evident in the similarity of the structure and function of their central nervous systems, rendering such species uniquely valuable for neuroscience research. Recently, the development of several genetically modified NHP models of NDs has successfully recapitulated key pathologies and revealed novel mechanisms. This review focuses on the efficacy of NHPs in modeling NDs and the novel pathological insights gained, as well as the challenges associated with the generation of such models and the complexities involved in their subsequent analysis.
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Affiliation(s)
- Ming-Tian Pan
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong 510632, China
| | - Han Zhang
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong 510632, China
| | - Xiao-Jiang Li
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong 510632, China
| | - Xiang-Yu Guo
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong 510632, China. E-mail:
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Dalton GD, Siecinski SK, Nikolova VD, Cofer GP, Hornburg K, Qi Y, Johnson GA, Jiang YH, Moy SS, Gregory SG. Transcriptome Analysis Identifies An ASD-Like Phenotype In Oligodendrocytes And Microglia From C58/J Amygdala That Is Dependent On Sex and Sociability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575733. [PMID: 38293238 PMCID: PMC10827122 DOI: 10.1101/2024.01.15.575733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Background Autism Spectrum Disorder (ASD) is a group of neurodevelopmental disorders with higher incidence in males and is characterized by atypical verbal/nonverbal communication, restricted interests that can be accompanied by repetitive behavior, and disturbances in social behavior. This study investigated brain mechanisms that contribute to sociability deficits and sex differences in an ASD animal model. Methods Sociability was measured in C58/J and C57BL/6J mice using the 3-chamber social choice test. Bulk RNA-Seq and snRNA-Seq identified transcriptional changes in C58/J and C57BL/6J amygdala within which DMRseq was used to measure differentially methylated regions in amygdala. Results C58/J mice displayed divergent social strata in the 3-chamber test. Transcriptional and pathway signatures revealed immune-related biological processes differ between C58/J and C57BL/6J amygdala. Hypermethylated and hypomethylated genes were identified in C58/J versus C57BL/6J amygdala. snRNA-Seq data in C58/J amygdala identified differential transcriptional signatures within oligodendrocytes and microglia characterized by increased ASD risk gene expression and predicted impaired myelination that was dependent on sex and sociability. RNA velocity, gene regulatory network, and cell communication analysis showed diminished oligodendrocyte/microglia differentiation. Findings were verified using bulk RNA-Seq and demonstrated oxytocin's beneficial effects on myelin gene expression. Limitations Our findings are significant. However, limitations can be noted. The cellular mechanisms linking reduced oligodendrocyte differentiation and reduced myelination to an ASD phenotype in C58/J mice need further investigation. Additional snRNA-Seq and spatial studies would determine if effects in oligodendrocytes/microglia are unique to amygdala or if this occurs in other brain regions. Oxytocin's effects need further examination to understand its potential as an ASD therapeutic. Conclusions Our work demonstrates the C58/J mouse model's utility in evaluating the influence of sex and sociability on the transcriptome in concomitant brain regions involved in ASD. Our single-nucleus transcriptome analysis elucidates potential pathological roles of oligodendrocytes and microglia in ASD. This investigation provides details regarding regulatory features disrupted in these cell types, including transcriptional gene dysregulation, aberrant cell differentiation, altered gene regulatory networks, and changes to key pathways that promote microglia/oligodendrocyte differentiation. Our studies provide insight into interactions between genetic risk and epigenetic processes associated with divergent affiliative behavior and lack of positive sociability.
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Modo M, Sparling K, Novotny J, Perry N, Foley LM, Hitchens TK. Mapping mesoscale connectivity within the human hippocampus. Neuroimage 2023; 282:120406. [PMID: 37827206 PMCID: PMC10623761 DOI: 10.1016/j.neuroimage.2023.120406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/28/2023] [Accepted: 10/10/2023] [Indexed: 10/14/2023] Open
Abstract
The connectivity of the hippocampus is essential to its functions. To gain a whole system view of intrahippocampal connectivity, ex vivo mesoscale (100 μm isotropic resolution) multi-shell diffusion MRI (11.7T) and tractography were performed on entire post-mortem human right hippocampi. Volumetric measurements indicated that the head region was largest followed by the body and tail regions. A unique anatomical organization in the head region reflected a complex organization of the granule cell layer (GCL) of the dentate gyrus. Tractography revealed the volumetric distribution of the perforant path, including both the tri-synaptic and temporoammonic pathways, as well as other well-established canonical connections, such as Schaffer collaterals. Visualization of the perforant path provided a means to verify the borders between the pro-subiculum and CA1, as well as between CA1/CA2. A specific angularity of different layers of fibers in the alveus was evident across the whole sample and allowed a separation of afferent and efferent connections based on their origin (i.e. entorhinal cortex) or destination (i.e. fimbria) using a cluster analysis of streamlines. Non-canonical translamellar connections running along the anterior-posterior axis were also discerned in the hilus. In line with "dentations" of the GCL, mossy fibers were bunching together in the sagittal plane revealing a unique lamellar organization and connections between these. In the head region, mossy fibers projected to the origin of the fimbria, which was distinct from the body and tail region. Mesoscale tractography provides an unprecedented systems view of intrahippocampal connections that underpin cognitive and emotional processing.
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Affiliation(s)
- Michel Modo
- Department of Radiology; Department of BioEngineering; McGowan Institute for Regenerative Medicine; Centre for Neuroscience University of Pittsburgh (CNUP); Centre for the Neural Basis of Cognition (CNBC).
| | | | | | | | | | - T Kevin Hitchens
- Small Animal Imaging Center; Departmnet of Neurobiology, University of Pittsburgh, Pittsburgh, PA 15203, USA
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Chowdhury R, Wan J, Gardier R, Rafael-Patino J, Thiran JP, Gibou F, Mukherjee A. Molecular Imaging with Aquaporin-Based Reporter Genes: Quantitative Considerations from Monte Carlo Diffusion Simulations. ACS Synth Biol 2023; 12:3041-3049. [PMID: 37793076 DOI: 10.1021/acssynbio.3c00372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
Aquaporins provide a unique approach for imaging genetic activity in deep tissues by increasing the rate of cellular water diffusion, which generates a magnetic resonance contrast. However, distinguishing aquaporin signals from the tissue background is challenging because water diffusion is influenced by structural factors, such as cell size and packing density. Here, we developed a Monte Carlo model to analyze how cell radius and intracellular volume fraction quantitatively affect aquaporin signals. We demonstrated that a differential imaging approach based on subtracting signals at two diffusion times can improve specificity by unambiguously isolating aquaporin signals from the tissue background. We further used Monte Carlo simulations to analyze the connection between diffusivity and the percentage of cells engineered to express aquaporin and established a mapping that accurately determined the volume fraction of aquaporin-expressing cells in mixed populations. The quantitative framework developed in this study will enable a broad range of applications in biomedical synthetic biology, requiring the use of aquaporins to noninvasively monitor the location and function of genetically engineered devices in live animals.
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Affiliation(s)
| | | | - Remy Gardier
- Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Jonathan Rafael-Patino
- Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Radiology Department, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne (UNIL), 1005 Lausanne, Switzerland
| | - Jean-Philippe Thiran
- Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Radiology Department, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne (UNIL), 1005 Lausanne, Switzerland
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Hurst CD, Dunn AR, Dammer EB, Duong DM, Shapley SM, Seyfried NT, Kaczorowski CC, Johnson ECB. Genetic background influences the 5XFAD Alzheimer's disease mouse model brain proteome. Front Aging Neurosci 2023; 15:1239116. [PMID: 37901791 PMCID: PMC10602695 DOI: 10.3389/fnagi.2023.1239116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/12/2023] [Indexed: 10/31/2023] Open
Abstract
There is an urgent need to improve the translational validity of Alzheimer's disease (AD) mouse models. Introducing genetic background diversity in AD mouse models has been proposed as a way to increase validity and enable the discovery of previously uncharacterized genetic contributions to AD susceptibility or resilience. However, the extent to which genetic background influences the mouse brain proteome and its perturbation in AD mouse models is unknown. In this study, we crossed the 5XFAD AD mouse model on a C57BL/6J (B6) inbred background with the DBA/2J (D2) inbred background and analyzed the effects of genetic background variation on the brain proteome in F1 progeny. Both genetic background and 5XFAD transgene insertion strongly affected protein variance in the hippocampus and cortex (n = 3,368 proteins). Protein co-expression network analysis identified 16 modules of highly co-expressed proteins common across the hippocampus and cortex in 5XFAD and non-transgenic mice. Among the modules strongly influenced by genetic background were those related to small molecule metabolism and ion transport. Modules strongly influenced by the 5XFAD transgene were related to lysosome/stress responses and neuronal synapse/signaling. The modules with the strongest relationship to human disease-neuronal synapse/signaling and lysosome/stress response-were not significantly influenced by genetic background. However, other modules in 5XFAD that were related to human disease, such as GABA synaptic signaling and mitochondrial membrane modules, were influenced by genetic background. Most disease-related modules were more strongly correlated with AD genotype in the hippocampus compared with the cortex. Our findings suggest that the genetic diversity introduced by crossing B6 and D2 inbred backgrounds influences proteomic changes related to disease in the 5XFAD model, and that proteomic analysis of other genetic backgrounds in transgenic and knock-in AD mouse models is warranted to capture the full range of molecular heterogeneity in genetically diverse models of AD.
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Affiliation(s)
- Cheyenne D. Hurst
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States
| | - Amy R. Dunn
- Department of Mammalian Genetics, The Jackson Laboratory, Bar Harbor, ME, United States
| | - Eric B. Dammer
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States
| | - Duc M. Duong
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States
| | - Sarah M. Shapley
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States
| | - Nicholas T. Seyfried
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States
| | - Catherine C. Kaczorowski
- Department of Mammalian Genetics, The Jackson Laboratory, Bar Harbor, ME, United States
- Department of Neurology, The University of Michigan, Ann Arbor, MI, United States
| | - Erik C. B. Johnson
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, United States
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States
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Tian Y, Johnson GA, Williams RW, White LE. A rapid workflow for neuron counting in combined light sheet microscopy and magnetic resonance histology. Front Neurosci 2023; 17:1223226. [PMID: 37841684 PMCID: PMC10569694 DOI: 10.3389/fnins.2023.1223226] [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: 05/15/2023] [Accepted: 09/04/2023] [Indexed: 10/17/2023] Open
Abstract
Information on regional variation in cell numbers and densities in the CNS provides critical insight into structure, function, and the progression of CNS diseases. However, variability can be real or a consequence of methods that do not account for technical biases, including morphologic deformations, errors in the application of cell type labels and boundaries of regions, errors of counting rules and sampling sites. We address these issues in a mouse model by introducing a workflow that consists of the following steps: 1. Magnetic resonance histology (MRH) to establish the size, shape, and regional morphology of the mouse brain in situ. 2. Light-sheet microscopy (LSM) to selectively label neurons or other cells in the entire brain without sectioning artifacts. 3. Register LSM volumes to MRH volumes to correct for dissection errors and both global and regional deformations. 4. Implement stereological protocols for automated sampling and counting of cells in 3D LSM volumes. This workflow can analyze the cell densities of one brain region in less than 1 min and is highly replicable in cortical and subcortical gray matter regions and structures throughout the brain. This method demonstrates the advantage of not requiring an extensive amount of training data, achieving a F1 score of approximately 0.9 with just 20 training nuclei. We report deformation-corrected neuron (NeuN) counts and neuronal density in 13 representative regions in 5 C57BL/6J cases and 2 BXD strains. The data represent the variability among specimens for the same brain region and across regions within the specimen. Neuronal densities estimated with our workflow are within the range of values in previous classical stereological studies. We demonstrate the application of our workflow to a mouse model of aging. This workflow improves the accuracy of neuron counting and the assessment of neuronal density on a region-by-region basis, with broad applications for studies of how genetics, environment, and development across the lifespan impact cell numbers in the CNS.
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Affiliation(s)
- Yuqi Tian
- Duke Center for In Vivo Microscopy, Department of Radiology, Duke University, Durham, NC, United States
| | - G. Allan Johnson
- Duke Center for In Vivo Microscopy, Department of Radiology, Duke University, Durham, NC, United States
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Leonard E. White
- Department of Neurology, Duke University, Durham, NC, United States
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10
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Kronman FA, Liwang JK, Betty R, Vanselow DJ, Wu YT, Tustison NJ, Bhandiwad A, Manjila SB, Minteer JA, Shin D, Lee CH, Patil R, Duda JT, Puelles L, Gee JC, Zhang J, Ng L, Kim Y. Developmental Mouse Brain Common Coordinate Framework. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.14.557789. [PMID: 37745386 PMCID: PMC10515964 DOI: 10.1101/2023.09.14.557789] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
3D standard reference brains serve as key resources to understand the spatial organization of the brain and promote interoperability across different studies. However, unlike the adult mouse brain, the lack of standard 3D reference atlases for developing mouse brains has hindered advancement of our understanding of brain development. Here, we present a multimodal 3D developmental common coordinate framework (DevCCF) spanning mouse embryonic day (E) 11.5, E13.5, E15.5, E18.5, and postnatal day (P) 4, P14, and P56 with anatomical segmentations defined by a developmental ontology. At each age, the DevCCF features undistorted morphologically averaged atlas templates created from Magnetic Resonance Imaging and co-registered high-resolution templates from light sheet fluorescence microscopy. Expert-curated 3D anatomical segmentations at each age adhere to an updated prosomeric model and can be explored via an interactive 3D web-visualizer. As a use case, we employed the DevCCF to unveil the emergence of GABAergic neurons in embryonic brains. Moreover, we integrated the Allen CCFv3 into the P56 template with stereotaxic coordinates and mapped spatial transcriptome cell-type data with the developmental ontology. In summary, the DevCCF is an openly accessible resource that can be used for large-scale data integration to gain a comprehensive understanding of brain development.
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Affiliation(s)
- Fae A Kronman
- Department of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA
| | - Josephine K Liwang
- Department of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA
| | - Rebecca Betty
- Department of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA
| | - Daniel J Vanselow
- Department of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA
| | - Yuan-Ting Wu
- Department of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA
| | - Nicholas J Tustison
- Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA
| | | | - Steffy B Manjila
- Department of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA
| | - Jennifer A Minteer
- Department of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA
| | - Donghui Shin
- Department of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA
| | - Choong Heon Lee
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, NY, USA
| | - Rohan Patil
- Department of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA
| | - Jeffrey T Duda
- Department of Radiology, Penn Image Computing and Science Lab, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Luis Puelles
- Department of Human Anatomy and Psychobiology, Faculty of Medicine, Universidad de Murcia, and Murcia Arrixaca Institute for Biomedical Research (IMIB) Murcia, Spain
| | - James C Gee
- Department of Radiology, Penn Image Computing and Science Lab, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jiangyang Zhang
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, NY, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Yongsoo Kim
- Department of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA
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11
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Bruckmaier F, Allert RD, Neuling NR, Amrein P, Littin S, Briegel KD, Schätzle P, Knittel P, Zaitsev M, Bucher DB. Imaging local diffusion in microstructures using NV-based pulsed field gradient NMR. SCIENCE ADVANCES 2023; 9:eadh3484. [PMID: 37595048 PMCID: PMC10438442 DOI: 10.1126/sciadv.adh3484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/20/2023] [Indexed: 08/20/2023]
Abstract
Understanding diffusion in microstructures plays a crucial role in many scientific fields, including neuroscience, medicine, or energy research. While magnetic resonance (MR) methods are the gold standard for diffusion measurements, spatial encoding in MR imaging has limitations. Here, we introduce nitrogen-vacancy (NV) center-based nuclear MR (NMR) spectroscopy as a powerful tool to probe diffusion within microscopic sample volumes. We have developed an experimental scheme that combines pulsed gradient spin echo (PGSE) with optically detected NV-NMR spectroscopy, allowing local quantification of molecular diffusion and flow. We demonstrate correlated optical imaging with spatially resolved PGSE NV-NMR experiments probing anisotropic water diffusion within an individual model microstructure. Our optically detected PGSE NV-NMR technique opens up prospects for extending the current capabilities of investigating diffusion processes with the future potential of probing single cells, tissue microstructures, or ion mobility in thin film materials for battery applications.
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Affiliation(s)
- Fleming Bruckmaier
- Department of Chemistry, TUM School of Natural Sciences, Technical University of Munich, 85748 Garching, Germany
| | - Robin D. Allert
- Department of Chemistry, TUM School of Natural Sciences, Technical University of Munich, 85748 Garching, Germany
| | - Nick R. Neuling
- Department of Chemistry, TUM School of Natural Sciences, Technical University of Munich, 85748 Garching, Germany
| | - Philipp Amrein
- Division of Medical Physics, Department of Diagnostic and Interventional Radiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian Littin
- Division of Medical Physics, Department of Diagnostic and Interventional Radiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Karl D. Briegel
- Department of Chemistry, TUM School of Natural Sciences, Technical University of Munich, 85748 Garching, Germany
| | - Philip Schätzle
- Department of Sustainable Systems Engineering (INATECH), University of Freiburg, Emmy-Noether-Str. 2, 79110 Freiburg, Germany
| | - Peter Knittel
- Fraunhofer Institute for Applied Solid State Physics, Tullastr. 72, 79108 Freiburg, Germany
| | - Maxim Zaitsev
- Division of Medical Physics, Department of Diagnostic and Interventional Radiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dominik B. Bucher
- Department of Chemistry, TUM School of Natural Sciences, Technical University of Munich, 85748 Garching, Germany
- Munich Center for Quantum Science and Technology (MCQST), Schellingstr. 4, 80799 München, Germany
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12
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Hurst CD, Dunn AR, Dammer EB, Duong DM, Seyfried NT, Kaczorowski CC, Johnson ECB. Genetic background influences the 5XFAD Alzheimer's disease mouse model brain proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.12.544646. [PMID: 37398142 PMCID: PMC10312637 DOI: 10.1101/2023.06.12.544646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
There is a pressing need to improve the translational validity of Alzheimer's disease (AD) mouse models. Introducing genetic background diversity in AD mouse models has been proposed as a way to increase validity and enable discovery of previously uncharacterized genetic contributions to AD susceptibility or resilience. However, the extent to which genetic background influences the mouse brain proteome and its perturbation in AD mouse models is unknown. Here we crossed the 5XFAD AD mouse model on a C57BL/6J (B6) inbred background with the DBA/2J (D2) inbred background and analyzed the effects of genetic background variation on the brain proteome in F1 progeny. Both genetic background and 5XFAD transgene insertion strongly affected protein variance in hippocampus and cortex (n=3,368 proteins). Protein co-expression network analysis identified 16 modules of highly co-expressed proteins common across hippocampus and cortex in 5XFAD and non-transgenic mice. Among the modules strongly influenced by genetic background were those related to small molecule metabolism and ion transport. Modules strongly influenced by the 5XFAD transgene were related to lysosome/stress response and neuronal synapse/signaling. The modules with the strongest relationship to human disease-neuronal synapse/signaling and lysosome/stress response-were not significantly influenced by genetic background. However, other modules in 5XFAD that were related to human disease, such as GABA synaptic signaling and mitochondrial membrane modules, were influenced by genetic background. Most disease-related modules were more strongly correlated to AD genotype in hippocampus compared to cortex. Our findings suggest that genetic diversity introduced by crossing B6 and D2 inbred backgrounds influences proteomic changes related to disease in the 5XFAD model, and that proteomic analysis of other genetic backgrounds in transgenic and knock-in AD mouse models is warranted to capture the full range of molecular heterogeneity in genetically diverse models of AD.
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Affiliation(s)
- Cheyenne D. Hurst
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322 USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Amy R. Dunn
- The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - Eric B. Dammer
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322 USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Duc M. Duong
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322 USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Nicholas T. Seyfried
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322 USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Catherine C. Kaczorowski
- The Jackson Laboratory, Bar Harbor, ME 04609 USA
- The University of Michigan, Ann Arbor, MI 48105 USA
| | - Erik C. B. Johnson
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA 30322 USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322 USA
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13
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Chowdhury R, Wan J, Gardier R, Rafael-Patino J, Thiran JP, Gibou F, Mukherjee A. Molecular imaging with aquaporin-based reporter genes: quantitative considerations from Monte Carlo diffusion simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544324. [PMID: 37333205 PMCID: PMC10274877 DOI: 10.1101/2023.06.09.544324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Aquaporins provide a new class of genetic tools for imaging molecular activity in deep tissues by increasing the rate of cellular water diffusion, which generates magnetic resonance contrast. However, distinguishing aquaporin contrast from the tissue background is challenging because water diffusion is also influenced by structural factors such as cell size and packing density. Here, we developed and experimentally validated a Monte Carlo model to analyze how cell radius and intracellular volume fraction quantitatively affect aquaporin signals. We demonstrated that a differential imaging approach based on time-dependent changes in diffusivity can improve specificity by unambiguously isolating aquaporin-driven contrast from the tissue background. Finally, we used Monte Carlo simulations to analyze the connection between diffusivity and the percentage of cells engineered to express aquaporin, and established a simple mapping that accurately determined the volume fraction of aquaporin-expressing cells in mixed populations. This study creates a framework for broad applications of aquaporins, particularly in biomedicine and in vivo synthetic biology, where quantitative methods to measure the location and performance of genetic devices in whole vertebrates are necessary.
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Affiliation(s)
- Rochishnu Chowdhury
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Jinyang Wan
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
| | - Remy Gardier
- Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jonathan Rafael-Patino
- Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Radiology Department, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Jean-Philippe Thiran
- Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Radiology Department, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Frederic Gibou
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106, USA
- Department of Computer Science, University of California, Santa Barbara, CA 93106, USA
| | - Arnab Mukherjee
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
- Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106, USA
- Biological Engineering, University of California, Santa Barbara, CA 93106, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
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14
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Yun J, Baldini L, Huang Y, Li E, Li H, Chacko AN, Miller AD, Wan J, Mukherjee A. Engineering ligand stabilized aquaporin reporters for magnetic resonance imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543364. [PMID: 37333371 PMCID: PMC10274688 DOI: 10.1101/2023.06.02.543364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Imaging transgene expression in live tissues requires reporters that are detectable with deeply penetrant modalities, such as magnetic resonance imaging (MRI). Here, we show that LSAqp1, a water channel engineered from aquaporin-1, can be used to create background-free, drug-gated, and multiplex images of gene expression using MRI. LSAqp1 is a fusion protein composed of aquaporin-1 and a degradation tag that is sensitive to a cell-permeable ligand, which allows for dynamic small molecule modulation of MRI signals. LSAqp1 improves specificity for imaging gene expression by allowing reporter signals to be conditionally activated and distinguished from the tissue background by difference imaging. In addition, by engineering destabilized aquaporin-1 variants with different ligand requirements, it is possible to image distinct cell types simultaneously. Finally, we expressed LSAqp1 in a tumor model and showed successful in vivo imaging of gene expression without background activity. LSAqp1 provides a conceptually unique approach to accurately measure gene expression in living organisms by combining the physics of water diffusion and biotechnology tools to control protein stability.
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Affiliation(s)
- Jason Yun
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
| | - Logan Baldini
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Yimeng Huang
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
| | - Eugene Li
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Honghao Li
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
| | - Asish N. Chacko
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
| | - Austin D.C. Miller
- Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Jinyang Wan
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
| | - Arnab Mukherjee
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
- Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106, USA
- Biological Engineering, University of California, Santa Barbara, CA 93106, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
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15
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Tian Y, Johnson GA, Williams RW, White L. A rapid workflow for neuron counting in combined light sheet microscopy and magnetic resonance histology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.17.540884. [PMID: 37292796 PMCID: PMC10245654 DOI: 10.1101/2023.05.17.540884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Information on regional variation in cell numbers and densities in the CNS provides critical insight into structure, function, and the progression of CNS diseases. However, variability can be real or can be a consequence of methods that do not account for technical biases, including morphologic deformations, errors in the application of cell type labels and boundaries of regions, errors of counting rules and sampling sites. We address these issues of by introducing a workflow that consists of the following steps: 1. Magnetic resonance histology (MRH) to establish the size, shape, and regional morphology of the mouse brain in situ. 2. Light-sheet microscopy (LSM) to selectively label all neurons or other cells in the entire brain without sectioning artifacts. 3. Register LSM volumes to MRH volumes to correct for dissection errors and morphological deformations. 4. Implement novel protocol for automated sampling and counting of cells in 3D LSM volumes. This workflow can analyze the cells density of one brain region in less than 1 min and is highly replicable to cortical and subcortical gray matter regions and structures throughout the brain. We report deformation-corrected neuron (NeuN) counts and neuronal density in 13 representative regions in 5 C57B6/6J and 2 BXD strains. The data represent the variability among cases for the same brain region and across regions within case. Our data are consistent with previous studies. We demonstrate the application of our workflow to a mouse model of aging. This workflow improves the accuracy of neuron counting and the assessment of neuronal density on a region-by-region basis, with broad applications in how genetics, environment, and development across the lifespan impact brain structure.
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16
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Rasia-Filho AA, Calcagnotto ME, von Bohlen Und Halbach O. Introduction: What Are Dendritic Spines? ADVANCES IN NEUROBIOLOGY 2023; 34:1-68. [PMID: 37962793 DOI: 10.1007/978-3-031-36159-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Dendritic spines are cellular specializations that greatly increase the connectivity of neurons and modulate the "weight" of most postsynaptic excitatory potentials. Spines are found in very diverse animal species providing neural networks with a high integrative and computational possibility and plasticity, enabling the perception of sensorial stimuli and the elaboration of a myriad of behavioral displays, including emotional processing, memory, and learning. Humans have trillions of spines in the cerebral cortex, and these spines in a continuum of shapes and sizes can integrate the features that differ our brain from other species. In this chapter, we describe (1) the discovery of these small neuronal protrusions and the search for the biological meaning of dendritic spines; (2) the heterogeneity of shapes and sizes of spines, whose structure and composition are associated with the fine-tuning of synaptic processing in each nervous area, as well as the findings that support the role of dendritic spines in increasing the wiring of neural circuits and their functions; and (3) within the intraspine microenvironment, the integration and activation of signaling biochemical pathways, the compartmentalization of molecules or their spreading outside the spine, and the biophysical properties that can affect parent dendrites. We also provide (4) examples of plasticity involving dendritic spines and neural circuits relevant to species survival and comment on (5) current research advancements and challenges in this exciting research field.
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Affiliation(s)
- Alberto A Rasia-Filho
- Department of Basic Sciences/Physiology and Graduate Program in Biosciences, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil
- Graduate Program in Neuroscience, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Maria Elisa Calcagnotto
- Graduate Program in Neuroscience, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Department of Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Graduate Program in Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Graduate Program in Psychiatry and Behavioral Science, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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