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Chen YC, Bäck NE, Zhen J, Xiong L, Komba M, Gloyn AL, MacDonald PE, Mains RE, Eipper BA, Verchere CB. Peptidylglycine alpha-amidating monooxygenase is important in mice for beta-cell cilia formation and insulin secretion but promotes diabetes risk through beta-cell independent mechanisms. Mol Metab 2025; 96:102123. [PMID: 40120979 PMCID: PMC12090325 DOI: 10.1016/j.molmet.2025.102123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Revised: 03/10/2025] [Accepted: 03/10/2025] [Indexed: 03/25/2025] Open
Abstract
OBJECTIVES Carriers of PAM (peptidylglycine alpha-amidating monooxygenase) coding variant alleles have reduced insulinogenic index, higher risk of developing type 2 diabetes (T2D), and islets from heterozygous carriers of the PAM p.Asp563Gly variant display reduced insulin secretion. Exactly how global PAM deficiency contributes to hyperglycemia remains unclear. PAM is the only enzyme capable of converting glycine-extended peptide hormones into amidated products. Like neuropeptide Y (NPY), α-melanocyte stimulating hormone (αMSH), and glucagon-like peptide 1 (GLP-1), islet amyloid polypeptide (IAPP), a beta cell peptide that forms islet amyloid in type 2 diabetes, is a PAM substrate. We hypothesized that Pam deficiency limited to beta cells would lead to reduced insulin secretion, prevent the production of amidated IAPP, and reveal the extent to which loss of Pam in β-cells could accelerate the onset of hyperglycemia in mice. METHODS PAM activity was assessed in human islets from donors based on their PAM genotype. We generated beta cell-specific Pam knockout (Ins1Cre/+, Pamfl/fl; βPamKO) mice and performed islet culture, histological, and metabolic assays to evaluate the physiological roles of Pam in beta cells. We analyzed human IAPP (hIAPP) amyloid fibril forming kinetics using synthetic amidated and non-amidated hIAPP peptides, and generated hIAPP knock-in beta cell-specific Pam knockout (hIAPPw/w βPamKO) mice to determine the impact of hIAPP amidation on islet amyloid burden, islet graft survival, and glucose tolerance. RESULTS PAM enzyme activity was significantly reduced in islets from donors with the PAM p. Asp563Gly T2D-risk allele. Islets from βPamKO mice had impaired second-phase glucose- and KCl-induced insulin secretion. Beta cells from βPamKO mice had larger dense-core granules and fewer and shorter cilia. Interestingly, non-amidated hIAPP was less fibrillogenic in vitro, and high glucose-treated hIAPPw/w βPamKO islets had reduced amyloid burden. Despite these changes in beta cell function, βPamKO mice were not more susceptible to diet-induced hyperglycemia. In vitro beta cell death and in vivo islet graft survival remained comparable between hIAPPw/w βPamKO and hIAPPw/w islets. Surprisingly, aged hIAPPw/w βPamKO mice had improved insulin secretion and glucose tolerance. CONCLUSIONS Eliminating Pam expression only in beta cells leads to morphological changes in insulin granules, reduced insulin secretion, reduced hIAPP amyloid burden and altered ciliogenesis. However, in mice beta-cell Pam deficiency has no impact on the development of diet- or hIAPP-induced hyperglycemia. Our data are consistent with current studies revealing ancient, highly conserved roles for peptidergic signaling in the coordination of the diverse signals needed to regulate fundamental processes such as glucose homeostasis.
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Affiliation(s)
- Yi-Chun Chen
- Department of Surgery, Faculty of Medicine, University of British Columbia & BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
| | - Nils E Bäck
- Department of Anatomy, Faculty of Medicine, University of Helsinki, PO Box 63 (Haartmaninkatu 8), 00014 University of Helsinki, Finland.
| | - Jenicia Zhen
- Department of Surgery, Faculty of Medicine, University of British Columbia & BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
| | - Lena Xiong
- Department of Surgery, Faculty of Medicine, University of British Columbia & BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Mitsuhiro Komba
- Department of Surgery, Faculty of Medicine, University of British Columbia & BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
| | - Anna L Gloyn
- Department of Pediatrics, Division of Endocrinology & Diabetes and Department of Genetics, Stanford School of Medicine, Stanford Research Park, 3165 Porter Drive, Stanford, CA, 94304, USA.
| | - Patrick E MacDonald
- Department of Pharmacology and Alberta Diabetes Institute, 6-126C Li Ka Shing Centre for Health Research Innovation, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
| | - Richard E Mains
- Department of Neuroscience, University of Connecticut Health Center, 263 Farmington Avenue, MC 3401, Farmington, CT, 06030-3401, USA.
| | - Betty A Eipper
- Department of Neuroscience, University of Connecticut Health Center, 263 Farmington Avenue, MC 3401, Farmington, CT, 06030-3401, USA.
| | - C Bruce Verchere
- Department of Surgery, Faculty of Medicine, University of British Columbia & BC Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada; Centre for Molecular Medicine and Therapeutics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
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2
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Daniel Huang Y, Jadav N, Rutter G, Szymanski L, Bostina M, Harland DP. A generalist deep-learning volume segmentation tool for volume electron microscopy of biological samples. J Struct Biol 2025:108214. [PMID: 40449855 DOI: 10.1016/j.jsb.2025.108214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Revised: 05/12/2025] [Accepted: 05/27/2025] [Indexed: 06/03/2025]
Abstract
We present the Volume Segmentation Tool (VST), a deep learning software tool that implements volumetric image segmentation in volume electron microscopy image stack data from a wide range of biological sample types. VST automates the handling of data preprocessing, data augmentation, and network building, as well as the configuration for model training, while adapting to the specific dataset. We have tried to make VST more accessible by designing it to operate entirely on local hardware and have provided a browser-based interface with additional features for visualizations of the networks and augmented datasets. VST can utilise contour map prediction to support instance segmentation on top of semantic segmentation. Through examples from various resin-embedded sample derived transmission electron microscopy and scanning electron microscopy datasets, we demonstrate that VST achieves state of the art performance compared to existing approaches.
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Affiliation(s)
- Yuyao Daniel Huang
- Department of Microbiology & Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Nickhil Jadav
- Department of Microbiology & Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Georgia Rutter
- Department of Microbiology & Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Lech Szymanski
- School of Computing, University of Otago, Dunedin 9016, New Zealand
| | - Mihnea Bostina
- Department of Microbiology & Immunology, University of Otago, Dunedin 9016, New Zealand.
| | - Duane P Harland
- Smart Foods & Bioproducts Science Group, AgResearch, Christchurch 7608, New Zealand; Biomolecular Interaction Centre (BIC), Te Pokapū Taunekeneke Rāpoi Ngota, New Zealand.
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3
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Heyn J, Gorgels A, Hense N, Gombert A, Buhl EM, Stark L, Vondenhoff S, Simon J, Noels H, Marx N, Goettsch C. GRP75 inhibition attenuates arterial calcification. Atherosclerosis 2025:119243. [PMID: 40410081 DOI: 10.1016/j.atherosclerosis.2025.119243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Revised: 04/21/2025] [Accepted: 05/13/2025] [Indexed: 05/25/2025]
Abstract
BACKGROUND AND AIMS Arterial calcification is a risk factor for cardiovascular mortality. The calcification process is driven by the osteogenic transition of vascular smooth muscle cells (SMCs), which release extracellular vesicles (EVs) that act as mineralization nucleation sites. While mitochondrial dysfunction and endoplasmic reticulum (ER) stress have been implicated in arterial calcification, the role of their contact sites remains unknown. Mitochondria-associated membranes (MAMs) are inter-organelle contacts connecting the outer mitochondrial membrane to the ER membrane through protein-protein interactions. This study investigated the role of Glucose-regulated protein 75 (GRP75), a MAM linker protein, in SMC calcification and EV cargo. METHODS Human coronary artery SMCs were cultured in osteogenic medium to induce calcification. MAMs were isolated from SMCs and human carotid artery by subcellular fractionation and visualized using transmission electron microscopy. SMC-derived EVs were isolated from the conditioned culture medium by ultracentrifugation. GRP75 inhibition was achieved using silencing RNA or the inhibitor MKT-077. Mitochondrial respiration and ER stress were analyzed using Seahorse analysis and Western blotting. RESULTS Calcifying SMCs expressed higher GRP75 mRNA (2.2-fold ± 0.7, p = 0.043) and protein (1.3-fold ± 0.2, p = 0.008) levels compared to control SMCs. GRP75 was enriched at MAMs, and electron microscopy imaging demonstrated closer mitochondria-ER contacts in both calcifying SMCs in vitro and human calcified carotid artery specimens. GRP75 inhibition by silencing RNA (-35 % ± 13 %, p < 0.001) or MKT-077 (-57 % ± 3 %, p < 0.001) attenuated matrix mineralization and reduced close mitochondria-ER contacts along with attenuating mitochondrial respiration capacity. Additionally, GRP75 was enriched in EVs released by calcifying SMCs (1.3-fold ± 0.1, p = 0.040). CONCLUSIONS Our findings demonstrate that MAMs are altered in calcifying SMCs. GRP75 inhibition disrupted close mitochondria-ER contact formation, decreased mitochondrial respiration, modulated the osteogenic transition of SMCs, and reduced vascular calcification. Therefore, GRP75 could serve as a potential target for preventing arterial calcification.
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Affiliation(s)
- Jonas Heyn
- Department of Internal Medicine I - Cardiology, Medical Faculty, Uniklinik RWTH Aachen, RWTH Aachen University, 52074, Aachen, Germany
| | - Andrea Gorgels
- Department of Internal Medicine I - Cardiology, Medical Faculty, Uniklinik RWTH Aachen, RWTH Aachen University, 52074, Aachen, Germany
| | - Nicolas Hense
- Department of Internal Medicine I - Cardiology, Medical Faculty, Uniklinik RWTH Aachen, RWTH Aachen University, 52074, Aachen, Germany
| | - Alexander Gombert
- Department of Vascular Surgery, Medical Faculty, Uniklinik RWTH Aachen, RWTH Aachen University, 52074, Aachen, Germany
| | - Eva Miriam Buhl
- Electron Microscopy Facility, Institute of Pathology, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany
| | - Lisa Stark
- Department of Internal Medicine I - Cardiology, Medical Faculty, Uniklinik RWTH Aachen, RWTH Aachen University, 52074, Aachen, Germany
| | - Sonja Vondenhoff
- Institute for Molecular Cardiovascular Research (IMCAR), Medical Faculty, Uniklinik RWTH Aachen, RWTH Aachen University, 52074, Aachen, Germany
| | - Joel Simon
- Department of Internal Medicine I - Cardiology, Medical Faculty, Uniklinik RWTH Aachen, RWTH Aachen University, 52074, Aachen, Germany
| | - Heidi Noels
- Institute for Molecular Cardiovascular Research (IMCAR), Medical Faculty, Uniklinik RWTH Aachen, RWTH Aachen University, 52074, Aachen, Germany
| | - Nikolaus Marx
- Department of Internal Medicine I - Cardiology, Medical Faculty, Uniklinik RWTH Aachen, RWTH Aachen University, 52074, Aachen, Germany
| | - Claudia Goettsch
- Department of Internal Medicine I - Cardiology, Medical Faculty, Uniklinik RWTH Aachen, RWTH Aachen University, 52074, Aachen, Germany; Institute of Physiology, Medical Faculty Carl Gustav Carus, Technical University Dresden, 01307, Dresden, Germany.
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4
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Szkalisity Á, Vanharanta L, Saito H, Vörös C, Li S, Isomäki A, Tomberg T, Strachan C, Belevich I, Jokitalo E, Ikonen E. Nuclear envelope-associated lipid droplets are enriched in cholesteryl esters and increase during inflammatory signaling. EMBO J 2025; 44:2774-2802. [PMID: 40195500 DOI: 10.1038/s44318-025-00423-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Revised: 03/04/2025] [Accepted: 03/11/2025] [Indexed: 04/09/2025] Open
Abstract
Cholesteryl esters (CEs) and triacylglycerols (TAGs) are stored in lipid droplets (LDs), but their compartmentalisation is not well understood. Here, we established a hyperspectral stimulated Raman scattering microscopy system to identify and quantitatively assess CEs and TAGs in individual LDs of human cells. We found that nuclear envelope-associated lipid droplets (NE-LDs) were enriched in cholesteryl esters compared to lipid droplets in the cytoplasm. Correlative light-volume-electron microscopy revealed that NE-LDs projected towards the cytoplasm and associated with type II nuclear envelope (NE) invaginations. The nuclear envelope localization of sterol O-acyltransferase 1 (SOAT1) contributed to NE-LD generation, as trapping of SOAT1 to the NE further increased their number. Upon stimulation by the pro-inflammatory cytokine TNFα, the number of NE-LDs moderately increased. Moreover, TNFα-induced NF-κB nuclear translocation was fine-tuned by SOAT1: increased SOAT1 activity and NE-LDs associated with faster NF-κB translocation, whereas reduced SOAT1 activity and NE-LDs associated with slower NF-κB translocation. Our findings suggest that the NE is enriched in CEs and that cholesterol esterification can modulate nuclear translocation.
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Affiliation(s)
- Ábel Szkalisity
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - Lauri Vanharanta
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - Hodaka Saito
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - Csaba Vörös
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
- Synthetic and Systems Biology Unit, Biological Research Centre (BRC), Hungarian Research Network (HUN-REN), 6726, Szeged, Hungary
| | - Shiqian Li
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - Antti Isomäki
- Biomedicum Imaging Unit, Department of Anatomy, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Teemu Tomberg
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, 00014, Helsinki, Finland
| | - Clare Strachan
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, 00014, Helsinki, Finland
| | - Ilya Belevich
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Elina Ikonen
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland.
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland.
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5
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Ohtonen S, Jäntti H, Giudice L, Mohamed A, Shakirzyanova A, Závodná T, Belevich I, Yan H, Sabogal-Guáqueta AM, Saveleva L, Väänänen MA, Rillo-Albert A, Perciballi E, Ferrari D, Tervo MM, Gómez-Budia M, Krejčík Z, Aakko-Saksa P, Koistinaho J, Lehtonen Š, Kanninen KM, Topinka J, Jokitalo E, Sierra A, Schmidt M, Dolga AM, Jalava PI, Korhonen P, Malm T. Traffic-related diesel pollution particles impair the lysosomal functions of human iPSC-derived microglia. ENVIRONMENT INTERNATIONAL 2025; 199:109467. [PMID: 40349663 DOI: 10.1016/j.envint.2025.109467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2024] [Revised: 03/14/2025] [Accepted: 04/13/2025] [Indexed: 05/14/2025]
Abstract
Exposure to air pollution is associated with neurological diseases. Traffic is a major source of air pollution, consisting of a complex mixture of ultrafine particles, that can invade the brain and induce a microglia-mediated inflammatory response. However, the exact mechanisms of how traffic-related particles impact human microglia remain poorly understood. This study investigates the effects of diesel exhaust particles (DEPs) on human induced pluripotent stem cell-derived microglia-like cells (iMGL). We exposed iMGLs to three different DEPs and studied the impact on the iMGL transcriptome and functionality, focusing on cytokine secretion, mitochondrial respiration, lysosomal function, and phagocytosis. A20 particles were collected from a heavy-duty engine run with petroleum diesel. For A0, the same engine was run with renewable diesel. E6 was produced with a modern 2019 model diesel passenger car run with renewable diesel. RNAseq revealed activation of the cytokine storm pathway and inhibition of the autophagy pathway in iMGLs after exposure to particles derived from older diesel emission technology (A20, A0). Particles from the modern diesel engine technology (E6) did not alter microglial transcriptome after 24 h exposure. A20 and A0 exposure led to impaired lysosomal functions in iMGLs. In contrast, E6 did not cause major alterations in microglia functions. In addition, we show that response to particles is more pronounced in human iMGLs compared to mouse primary microglia. To conclude, particles from older emission technology impair phago-lysosomal functions of iMGLs, but modern alternatives with filtration do not induce drastic changes in the functionality of iMGLs.
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Affiliation(s)
- Sohvi Ohtonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
| | - Henna Jäntti
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Luca Giudice
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ahmed Mohamed
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Anastasia Shakirzyanova
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Táňa Závodná
- Department of Toxicology and Molecular Epidemiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ilya Belevich
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Hong Yan
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, Faculty of Science and Engineering, University of Groningen, the Netherlands
| | - Angélica María Sabogal-Guáqueta
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, Faculty of Science and Engineering, University of Groningen, the Netherlands; Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Liudmila Saveleva
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Mari-Anna Väänänen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ashley Rillo-Albert
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Elisa Perciballi
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland; Department of Biotechnology and Bioscience, University of Milano-Bicocca, Milan, Italy
| | - Daniela Ferrari
- Department of Biotechnology and Bioscience, University of Milano-Bicocca, Milan, Italy
| | - Minna-Mari Tervo
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Mireia Gómez-Budia
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Zdeněk Krejčík
- Department of Toxicology and Molecular Epidemiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Jari Koistinaho
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Šárka Lehtonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Katja M Kanninen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Jan Topinka
- Department of Toxicology and Molecular Epidemiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Alejandra Sierra
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Martina Schmidt
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, Faculty of Science and Engineering, University of Groningen, the Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Amalia M Dolga
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, Faculty of Science and Engineering, University of Groningen, the Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Pasi I Jalava
- Department of Environmental and Biological Science, University of Eastern Finland, Kuopio, Finland
| | - Paula Korhonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
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Ueffing M, Langeheine M, Gniesmer S, Rode K, Staggenborg S, Wirth G, Rohn K, Koch R, Blume I, Pfarrer C, Wrede C, Brehm R. The impact of Connexin 43 deficiency on the cell shape and cytoskeleton of murine Sertoli cells: A house with ramshackle walls? PLoS One 2025; 20:e0321292. [PMID: 40273151 PMCID: PMC12021162 DOI: 10.1371/journal.pone.0321292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Accepted: 03/03/2025] [Indexed: 04/26/2025] Open
Abstract
Genetically induced loss of the gap-junction protein Connexin 43 (Cx43) in murine Sertoli cells leads to an arrest of spermatogenesis at the level of spermatogonia, highly vacuolated tubules, and intratubular cell clusters. Transmission electron microscopy as well as 3D-reconstruction of Sertoli cells based on serial block-face scanning electron microscopy imaging revealed severe cell shape changes in Cx43 deficient Sertoli cells. Since the cytoskeleton is important for the transport of germ cells within the seminiferous epithelium and for keeping the cell shape, the study at hand aimed to reveal correlations of Cx43 loss and changes of cytoskeletal components and their spatial organization in the seminiferous epithelium. Immunohistochemistry, immunofluorescence, conventional transmission electron microcopy and immunogold labeling indicated alterations in microtubule and actin filament distribution patterns in Cx43 deficient Sertoli cells compared to wildtype mice. Firstly, microtubules seemed to be misoriented in mutant Sertoli cells. Secondly, the actin filament based basal ectoplasmic specializations were increased in spatial extension, but the apical ectoplasmic specialization was missing. Lastly, Sertoli cells of both genotypes immunostained positive for vimentin, the prevalent intermediate filament of Sertoli cells, but not for keratins, markers for Sertoli cell immaturity or dedifferentiation. In conclusion, Cx43 deficiency in Sertoli cells correlates not only with severe cell shape alterations but also with changes in microtubule and actin filament distribution patterns, while intermediate filament expression seems to be only negligibly influenced.
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Affiliation(s)
- Mareike Ueffing
- Institute for Anatomy, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Marion Langeheine
- Institute for Anatomy, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Sarah Gniesmer
- Institute for Anatomy, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Kristina Rode
- Institute for Anatomy, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Sarah Staggenborg
- Institute for Anatomy, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Gudrun Wirth
- Institute for Anatomy, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Kerstin Rohn
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Rüdiger Koch
- Institute for Anatomy, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Ines Blume
- Institute for Anatomy, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Christiane Pfarrer
- Institute for Anatomy, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Christoph Wrede
- Research Core Unit Electron Microscopy, Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany
| | - Ralph Brehm
- Institute for Anatomy, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
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7
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Passini FS, Bornstein B, Rubin S, Kuperman Y, Krief S, Masschelein E, Mehlman T, Brandis A, Addadi Y, Shalom SHO, Richter EA, Yardeni T, Tirosh A, De Bock K, Zelzer E. Piezo2 in sensory neurons regulates systemic and adipose tissue metabolism. Cell Metab 2025; 37:987-1000.e6. [PMID: 39919739 DOI: 10.1016/j.cmet.2024.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 10/23/2024] [Accepted: 12/31/2024] [Indexed: 02/09/2025]
Abstract
Systemic metabolism ensures energy homeostasis through inter-organ crosstalk regulating thermogenic adipose tissue. Unlike the well-described inductive role of the sympathetic system, the inhibitory signal ensuring energy preservation remains poorly understood. Here, we show that, via the mechanosensor Piezo2, sensory neurons regulate morphological and physiological properties of brown and beige fat and prevent systemic hypermetabolism. Targeting runt-related transcription factor 3 (Runx3)/parvalbumin (PV) sensory neurons in independent genetic mouse models resulted in a systemic metabolic phenotype characterized by reduced body fat and increased insulin sensitivity and glucose tolerance. Deletion of Piezo2 in PV sensory neurons reproduced the phenotype, protected against high-fat-diet-induced obesity, and caused adipose tissue browning and beiging, likely driven by elevated norepinephrine levels. Finding that brown and beige fat are innervated by Runx3/PV sensory neurons expressing Piezo2 suggests a model in which mechanical signals, sensed by Piezo2 in sensory neurons, protect energy storage and prevent a systemic hypermetabolic phenotype.
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Affiliation(s)
- Fabian S Passini
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| | - Bavat Bornstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sarah Rubin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Kuperman
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Sharon Krief
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Evi Masschelein
- Department of Health Sciences and Technology, Laboratory of Exercise and Health, Swiss Federal Institute of Technology (ETH Zürich), Zurich, Switzerland
| | - Tevie Mehlman
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Brandis
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Yoseph Addadi
- MICC Cell Observatory, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Shira Huri-Ohev Shalom
- Bert Strassburger Metabolic Center for Preventive Medicine, Sheba Medical Center, Tel-Hashomer, Israel
| | - Erik A Richter
- Department of Nutrition, Exercise, and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Tal Yardeni
- Bert Strassburger Metabolic Center for Preventive Medicine, Sheba Medical Center, Tel-Hashomer, Israel
| | - Amir Tirosh
- The Dalia and David Arabov Endocrinology and Diabetes Research Center, Institute of Endocrinology, Sheba Medical Center, Tel-Hashomer, Israel; Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Katrien De Bock
- Department of Health Sciences and Technology, Laboratory of Exercise and Health, Swiss Federal Institute of Technology (ETH Zürich), Zurich, Switzerland
| | - Elazar Zelzer
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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8
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Depret N, Gleizes M, Moreau MM, Poirault-Chassac S, Quiedeville A, Carvalho SDS, Venugopal V, Abed ASA, Ezan J, Barthet G, Mulle C, Desmedt A, Marighetto A, Racca C, Montcouquiol M, Sans N. The correct connectivity of the DG-CA3 circuits involved in declarative memory processes depends on Vangl2-dependent planar cell polarity signaling. Prog Neurobiol 2025; 246:102728. [PMID: 39956311 DOI: 10.1016/j.pneurobio.2025.102728] [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: 09/24/2024] [Revised: 02/04/2025] [Accepted: 02/05/2025] [Indexed: 02/18/2025]
Abstract
In the hippocampus, dentate gyrus granule cells connect to CA3 pyramidal cells via their axons, the mossy fibers (Mf). The synaptic terminals of Mfs (Mf boutons, MfBs) form large and complex synapses with thorny excrescences (TE) on the proximal dendrites of CA3 pyramidal cells (PCs). MfB/TE synapses have distinctive "detonator" properties due to low initial release probability and large presynaptic facilitation. The molecular mechanisms shaping the morpho-functional properties of MfB/TE synapses are still poorly understood, though alterations in their morphology are associated with Down syndrome, intellectual disabilities, and Alzheimer's disease. Here, we identify the core PCP gene Vangl2 as essential to the morphogenesis and function of MfB/TE synapses. Vangl2 colocalises with the presynaptic heparan sulfate proteoglycan glypican 4 (GPC4) to stabilise the postsynaptic orphan receptor GPR158. Embryonic loss of Vangl2 disrupts the morphology of MfBs and TEs, impairs ultrastructural and molecular organisation, resulting in defective synaptic transmission and plasticity. In adult, the early loss of Vangl2 results in a number of hippocampus-dependent memory deficits including characteristic flexibility of declarative memory, organisation and retention of working / everyday-like memory. These deficits also lead to abnormal generalisation of memories to salient cues and diminished ability to form detailed contextual memories. Together, these results establish Vangl2 as a key regulator of DG-CA3 connectivity and functions.
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Affiliation(s)
- Noémie Depret
- Univ. Bordeaux, Inserm, Neurocentre Magendie, U1215, Bordeaux F-33000, France
| | - Marie Gleizes
- Univ. Bordeaux, Inserm, Neurocentre Magendie, U1215, Bordeaux F-33000, France
| | - Maïté Marie Moreau
- Univ. Bordeaux, Inserm, Neurocentre Magendie, U1215, Bordeaux F-33000, France
| | | | - Anne Quiedeville
- Univ. Bordeaux, Inserm, Neurocentre Magendie, U1215, Bordeaux F-33000, France
| | | | - Vasika Venugopal
- Univ. Bordeaux, Inserm, Neurocentre Magendie, U1215, Bordeaux F-33000, France
| | - Alice Shaam Al Abed
- Univ. Bordeaux, Inserm, Neurocentre Magendie, U1215, Bordeaux F-33000, France
| | - Jérôme Ezan
- Univ. Bordeaux, Inserm, Neurocentre Magendie, U1215, Bordeaux F-33000, France
| | - Gael Barthet
- Univ. Bordeaux, CNRS, IINS, UMR 5297, Bordeaux F-33000, France
| | | | - Aline Desmedt
- Univ. Bordeaux, Inserm, Neurocentre Magendie, U1215, Bordeaux F-33000, France
| | - Aline Marighetto
- Univ. Bordeaux, Inserm, Neurocentre Magendie, U1215, Bordeaux F-33000, France
| | - Claudia Racca
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Nathalie Sans
- Univ. Bordeaux, Inserm, Neurocentre Magendie, U1215, Bordeaux F-33000, France.
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9
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Nilsson CI, Dumral Ö, Sanchez G, Xie B, Müller A, Solimena M, Ren H, Idevall-Hagren O. Somatostatin triggers local cAMP and Ca 2+ signaling in primary cilia to modulate pancreatic β-cell function. EMBO J 2025; 44:1663-1691. [PMID: 39939781 PMCID: PMC11914567 DOI: 10.1038/s44318-025-00383-7] [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: 06/24/2024] [Revised: 01/15/2025] [Accepted: 01/29/2025] [Indexed: 02/14/2025] Open
Abstract
Somatostatin, released from δ-cells within pancreatic islets of Langerhans, is one of the most important negative regulators of islet hormone secretion. We find that islet δ-cells are positioned near, and release somatostatin onto, primary cilia of the other islet cell types, including insulin-secreting β-cells. Somatostatin activates ciliary somatostatin receptors, resulting in rapid lowering of the ciliary cAMP concentration which in turn promotes more sustained nuclear translocation of the cilia-dependent transcription factor GLI2 through a mechanism that operates in parallel with the canonical Hedgehog pathway and depends on ciliary Ca2+ signaling. We also find that primary cilia length is reduced in islets from human donors with type-2 diabetes, which is associated with a reduction in interactions between δ-cells and cilia. Our findings show that islet cell primary cilia constitute an important target of somatostatin action, which endows somatostatin with the ability to regulate islet cell function beyond acute suppression of hormone release.
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Affiliation(s)
- Ceren Incedal Nilsson
- Department of Medical Cell Biology, Uppsala University, BMC Box 571, 75123, Uppsala, Sweden
| | - Özge Dumral
- Department of Medical Cell Biology, Uppsala University, BMC Box 571, 75123, Uppsala, Sweden
| | - Gonzalo Sanchez
- Department of Medical Cell Biology, Uppsala University, BMC Box 571, 75123, Uppsala, Sweden
| | - Beichen Xie
- Center for Quantitative Biology, Peking University, 100871, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Andreas Müller
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Michele Solimena
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Huixia Ren
- Center for Quantitative Biology, Peking University, 100871, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Olof Idevall-Hagren
- Department of Medical Cell Biology, Uppsala University, BMC Box 571, 75123, Uppsala, Sweden.
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10
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Kichuk T, Avalos JL. Shape Matters: The Utility and Analysis of Altered Yeast Mitochondrial Morphology in Health, Disease, and Biotechnology. Int J Mol Sci 2025; 26:2152. [PMID: 40076772 PMCID: PMC11899761 DOI: 10.3390/ijms26052152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Revised: 01/28/2025] [Accepted: 01/30/2025] [Indexed: 03/14/2025] Open
Abstract
Mitochondria are involved in a wide array of critical cellular processes from energy production to cell death. The morphology (size and shape) of mitochondrial compartments is highly responsive to both intracellular and extracellular conditions, making these organelles highly dynamic. Nutrient levels and stressors both inside and outside the cell inform the balance of mitochondrial fission and fusion and the recycling of mitochondrial components known as mitophagy. The study of mitochondrial morphology and its implications in human disease and microbial engineering have gained significant attention over the past decade. The yeast Saccharomyces cerevisiae offers a valuable model system for studying mitochondria due to its ability to survive without respiring, its genetic tractability, and the high degree of mitochondrial similarity across eukaryotic species. Here, we review how the interplay between mitochondrial fission, fusion, biogenesis, and mitophagy regulates the dynamic nature of mitochondrial networks in both yeast and mammalian systems with an emphasis on yeast as a model organism. Additionally, we examine the crucial role of inter-organelle interactions, particularly between mitochondria and the endoplasmic reticulum, in regulating mitochondrial dynamics. The dysregulation of any of these processes gives rise to abnormal mitochondrial morphologies, which serve as the distinguishing features of numerous diseases, including Parkinson's disease, Alzheimer's disease, and cancer. Notably, yeast models have contributed to revealing the underlying mechanisms driving these human disease states. In addition to furthering our understanding of pathologic processes, aberrant yeast mitochondrial morphologies are of increasing interest to the seemingly distant field of metabolic engineering, following the discovery that compartmentalization of certain biosynthetic pathways within mitochondria can significantly improve chemical production. In this review, we examine the utility of yeast as a model organism to study mitochondrial morphology in both healthy and pathologic states, explore the nascent field of mitochondrial morphology engineering, and discuss the methods available for the quantification and classification of these key mitochondrial morphologies.
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Affiliation(s)
- Therese Kichuk
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA;
- Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA
| | - José L. Avalos
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA;
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ 08544, USA
- The Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ 08544, USA
- High Meadows Environmental Institute, Princeton University, Princeton, NJ 08544, USA
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11
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Adams R, Afzal N, Jafri MS, Mannella CA. How the Topology of the Mitochondrial Inner Membrane Modulates ATP Production. Cells 2025; 14:257. [PMID: 39996730 PMCID: PMC11853683 DOI: 10.3390/cells14040257] [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: 12/30/2024] [Revised: 01/31/2025] [Accepted: 02/06/2025] [Indexed: 02/26/2025] Open
Abstract
Cells in heart muscle need to generate ATP at or near peak capacity to meet their energy demands. Over 90% of this ATP comes from mitochondria, strategically located near myofibrils and densely packed with cristae to concentrate ATP generation per unit volume. However, a consequence of dense inner membrane (IM) packing is that restricted metabolite diffusion inside mitochondria may limit ATP production. Under physiological conditions, the flux of ATP synthase is set by ADP levels in the matrix, which in turn depends on diffusion-dependent concentration of ADP inside cristae. Computer simulations show how ADP diffusion and consequently rates of ATP synthesis are modulated by IM topology, in particular (i) number, size, and positioning of crista junctions that connect cristae to the IM boundary region, and (ii) branching of cristae. Predictions are compared with the actual IM topology of a cardiomyocyte mitochondrion in which cristae vary systematically in length and morphology. The analysis indicates that this IM topology decreases but does not eliminate the "diffusion penalty" on ATP output. It is proposed that IM topology normally attenuates mitochondrial ATP output under conditions of low workload and can be regulated by the cell to better match ATP supply to demand.
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Affiliation(s)
- Raquel Adams
- School of Systems Biology, George Mason University, Fairfax, VA 22030, USA; (R.A.); (N.A.)
| | - Nasrin Afzal
- School of Systems Biology, George Mason University, Fairfax, VA 22030, USA; (R.A.); (N.A.)
| | - Mohsin Saleet Jafri
- School of Systems Biology, George Mason University, Fairfax, VA 22030, USA; (R.A.); (N.A.)
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD 20201, USA
| | - Carmen A. Mannella
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD 20201, USA
- Department of Pharmacology, Physiology and Drug Development, University of Maryland School of Medicine, Baltimore, MD 20201, USA
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12
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Ezure T, Matsuzaki K, Urakubo H, Ohno N. Three-dimensional ultrastructural analysis of human skin with the arrector pili muscle interacting with the hair follicle epithelium. Sci Rep 2025; 15:4195. [PMID: 39905217 PMCID: PMC11794863 DOI: 10.1038/s41598-025-88615-y] [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: 10/23/2024] [Accepted: 01/29/2025] [Indexed: 02/06/2025] Open
Abstract
This study developed a three-dimensional ultrastructural analysis application using serial block-face scanning electron microscopy (SBF-SEM) to investigate surgically acquired human skin tissues containing the arrector pili muscle. We utilized the en bloc staining, including reduced osmium, thiocarbohydrazide, and lead aspartate, as well as the embedding using a carbon-based conductive resin. Next, we obtained serial images with SBF-SEM. The results revealed dense nerve fiber networks branching from nearby nerve fiber bundles outside the muscle and running among muscle fibers. Additionally, the dense nerve network running through and along arrector pili muscle fibers rarely penetrates the connective tissues between smooth muscle fibers and epithelial cells. Furthermore, in the observation area, no individual smooth muscle fibers formed adhesion structures with the epithelial cells of the hair follicle, ending in the dermal extracellular matrix near the epithelial cells. These results indicate the usefulness of this approach for three-dimensional ultrastructural analyses of human skin tissues comprising follicular units and revealing structural changes in skin tissues, especially the arrector pili muscle and nerve fibers with hair follicular epithelium, in aging and diseased conditions.
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Affiliation(s)
- Tomonobu Ezure
- MIRAI Technology Institute, Shiseido Co., Ltd, Yokohama, Kanagawa, Japan.
| | - Kyoichi Matsuzaki
- Department of Plastic and Reconstructive Surgery, School of Medicine, International University of Health and Welfare, Narita, Japan
| | - Hidetoshi Urakubo
- Section of Electron Microscopy, National Institute for Physiological Sciences, Okazaki, Aichi, Japan
| | - Nobuhiko Ohno
- Division of Ultrastructural Research, National Institute for Physiological Sciences, Okazaki, Aichi, Japan.
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13
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Schuhmann F, Akkaya KC, Puchkov D, Hohensee S, Lehmann M, Liu F, Pezeshkian W. Integrative Molecular Dynamics Simulations Untangle Cross-Linking Data to Unveil Mitochondrial Protein Distributions. Angew Chem Int Ed Engl 2025; 64:e202417804. [PMID: 39644219 DOI: 10.1002/anie.202417804] [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: 09/16/2024] [Revised: 11/14/2024] [Accepted: 11/26/2024] [Indexed: 12/09/2024]
Abstract
Cross-linking mass spectrometry (XL-MS) enables the mapping of protein-protein interactions on the cellular level. When applied to all compartments of mitochondria, the sheer number of cross-links and connections can be overwhelming, rendering simple cluster analyses convoluted and uninformative. To address this limitation, we integrate the XL-MS data, 3D electron microscopy data, and localization annotations with a supra coarse-grained molecular dynamics simulation to sort all data, making clusters more accessible and interpretable. In the context of mitochondria, this method, through a total of 6.9 milliseconds of simulations, successfully identifies known, suggests unknown protein clusters, and reveals the distribution of inner mitochondrial membrane proteins allowing a more precise localization within compartments. Our integrative approach suggests, that two so-far ambigiously placed proteins FAM162A and TMEM126A are localized in the cristae, which is validated through super resolution microscopy. Together, this demonstrates the strong potential of the presented approach.
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Affiliation(s)
- Fabian Schuhmann
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100, Copenhagen, Denmark
| | - Kerem Can Akkaya
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125, Berlin, Germany
- Department of Molecular Physiology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125, Berlin, Germany
| | - Dmytro Puchkov
- Department of Molecular Physiology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125, Berlin, Germany
| | - Svea Hohensee
- Department of Molecular Physiology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125, Berlin, Germany
| | - Martin Lehmann
- Department of Molecular Physiology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125, Berlin, Germany
| | - Fan Liu
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Charitépl. 1, 10117, Berlin, Germany
| | - Weria Pezeshkian
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100, Copenhagen, Denmark
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14
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Abdollahzadeh A, Coronado-Leija R, Lee HH, Sierra A, Fieremans E, Novikov DS. Scattering approach to diffusion quantifies axonal damage in brain injury. ARXIV 2025:arXiv:2501.18167v1. [PMID: 39975429 PMCID: PMC11838777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Early diagnosis and noninvasive monitoring of neurological disorders require sensitivity to elusive cellular-level alterations that occur much earlier than volumetric changes observable with the millimeter-resolution of medical imaging modalities. Morphological changes in axons, such as axonal varicosities or beadings, are observed in neurological disorders, as well as in development and aging. Here, we reveal the sensitivity of time-dependent diffusion MRI (dMRI) to axonal morphology at the micrometer scale. Scattering theory uncovers the two parameters that determine the diffusive dynamics of water in axons: the average reciprocal cross-section and the variance of long-range cross-sectional fluctuations. This theoretical development allowed us to predict dMRI metrics sensitive to axonal alterations across tens of thousands of axons in seconds rather than months of simulations in a rat model of traumatic brain injury. Our approach bridges the gap between micrometers and millimeters in resolution, offering quantitative, objective biomarkers applicable to a broad spectrum of neurological disorders.
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Affiliation(s)
- Ali Abdollahzadeh
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ricardo Coronado-Leija
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA
| | - Hong-Hsi Lee
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Alejandra Sierra
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Els Fieremans
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA
| | - Dmitry S. Novikov
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA
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15
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Savatović S, Laundon D, De Marco F, Riedel M, Hammel JU, Busse M, Salomé M, Pascolo L, Zanette I, Lewis RM, Herzen J, Thibault P. High-resolution X-ray phase-contrast tomography of human placenta with different wavefront markers. Sci Rep 2025; 15:2131. [PMID: 39820007 PMCID: PMC11739398 DOI: 10.1038/s41598-025-85105-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Accepted: 01/01/2025] [Indexed: 01/19/2025] Open
Abstract
Phase-contrast micro-tomography ([Formula: see text]CT) with synchrotron radiation can aid in the differentiation of subtle density variations in weakly absorbing soft tissue specimens. Modulation-based imaging (MBI) extracts phase information from the distortion of reference patterns, generated by periodic or randomly structured wavefront markers (e.g., gratings or sandpaper). The two approaches have already found application for the virtual inspection of biological samples. Here, we perform high-resolution [Formula: see text]CT scans of an unstained human placenta specimen, using MBI with both a 2D grating and sandpaper as modulators, as well as conventional propagation-based imaging (PBI). The 3D virtual representation of placenta offers a valuable tool for analysing its intricate branching villous network and vascular structure, providing new insights into its complex architecture. Within this study, we assess reconstruction quality achieved with all three evaluated phase-contrast methods. Both MBI datasets are processed with the Unified Modulated Pattern Analysis (UMPA) model, a pattern-matching algorithm. In order to evaluate the benefits and suitability of MBI for virtual histology, we discuss how the complexities of the technique influence image quality and correlate the obtained volumes to 2D techniques, such as conventional histology and X-ray fluorescence (XRF) elemental maps.
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Affiliation(s)
- Sara Savatović
- Munich Institute of Biomedical Engineering, Technical University of Munich, 85748, Garching, Germany.
- Research Group Biomedical Imaging Physics, Department of Physics, TUM School of Natural Sciences, Technical University of Munich, 85748, Garching, Germany.
- Chair of Biomedical Physics, Department of Physics, TUM School of Natural Sciences, Technical University of Munich, 85748, Garching, Germany.
- Department of Physics, University of Trieste, 34127, Trieste, Italy.
- Elettra - Sincrotrone Trieste S.C.p.A., 34149, Basovizza, Italy.
| | - Davis Laundon
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ, UK
- Institute for Life Sciences, University of Southampton, University Rd, Southampton, SO17 1BJ, UK
| | - Fabio De Marco
- Department of Physics, University of Trieste, 34127, Trieste, Italy
- Elettra - Sincrotrone Trieste S.C.p.A., 34149, Basovizza, Italy
| | - Mirko Riedel
- Munich Institute of Biomedical Engineering, Technical University of Munich, 85748, Garching, Germany
- Research Group Biomedical Imaging Physics, Department of Physics, TUM School of Natural Sciences, Technical University of Munich, 85748, Garching, Germany
- Chair of Biomedical Physics, Department of Physics, TUM School of Natural Sciences, Technical University of Munich, 85748, Garching, Germany
- Institute of Materials Physics, Helmholtz-Zentrum hereon, 21502, Geesthacht, Germany
| | - Jörg U Hammel
- Institute of Materials Physics, Helmholtz-Zentrum hereon, 21502, Geesthacht, Germany
| | - Madleen Busse
- Munich Institute of Biomedical Engineering, Technical University of Munich, 85748, Garching, Germany
- Chair of Biomedical Physics, Department of Physics, TUM School of Natural Sciences, Technical University of Munich, 85748, Garching, Germany
| | - Murielle Salomé
- ESRF - The European Synchrotron Radiation Facility, 38043, Grenoble, France
| | - Lorella Pascolo
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137, Trieste, Italy
| | - Irene Zanette
- Elettra - Sincrotrone Trieste S.C.p.A., 34149, Basovizza, Italy
| | - Rohan M Lewis
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ, UK
- Institute for Life Sciences, University of Southampton, University Rd, Southampton, SO17 1BJ, UK
| | - Julia Herzen
- Munich Institute of Biomedical Engineering, Technical University of Munich, 85748, Garching, Germany
- Research Group Biomedical Imaging Physics, Department of Physics, TUM School of Natural Sciences, Technical University of Munich, 85748, Garching, Germany
- Chair of Biomedical Physics, Department of Physics, TUM School of Natural Sciences, Technical University of Munich, 85748, Garching, Germany
| | - Pierre Thibault
- Department of Physics, University of Trieste, 34127, Trieste, Italy
- Elettra - Sincrotrone Trieste S.C.p.A., 34149, Basovizza, Italy
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16
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Faitg J, Davey T, Laws R, Lawless C, Tuppen H, Fitton E, Turnbull D, Vincent AE. Mapping mitochondrial morphology and function: COX-SBFSEM reveals patterns in mitochondrial disease. Commun Biol 2025; 8:24. [PMID: 39789156 PMCID: PMC11718190 DOI: 10.1038/s42003-024-07389-7] [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: 02/27/2024] [Accepted: 12/09/2024] [Indexed: 01/12/2025] Open
Abstract
Mitochondria play a crucial role in maintaining cellular health. It is interesting that the shape of mitochondria can vary depending on the type of cell, mitochondrial function, and other cellular conditions. However, there are limited studies that link functional assessment with mitochondrial morphology evaluation at high magnification, even fewer that do so in situ and none in human muscle biopsies. Therefore, we have developed a method which combines functional assessment of mitochondria through Cytochrome c Oxidase (COX) histochemistry, with a 3D electron microscopy (EM) technique, serial block-face scanning electron microscopy (SBFSEM). Here we apply COX-SBFSEM to muscle samples from patients with single, large-scale mtDNA deletions, a cause of mitochondrial disease. These deletions cause oxidative phosphorylation deficiency, which can be observed through changes in COX activity. One of the main advantages of combining 3D-EM with the COX reaction is the ability to look at how per-mitochondrion oxidative phosphorylation status is spatially distributed within muscle fibres. Here we show a robust spatial pattern in COX-positive and intermediate-fibres and that the spatial pattern is less clear in COX-deficient fibres.
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Affiliation(s)
- Julie Faitg
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
- Electron Microscopy Research Services, Newcastle University, Newcastle, UK
| | - Tracey Davey
- Electron Microscopy Research Services, Newcastle University, Newcastle, UK
| | - Ross Laws
- Electron Microscopy Research Services, Newcastle University, Newcastle, UK
| | - Conor Lawless
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
- NIHR Biomedical Research Centre Research Centre, Translational and Clinical Research, Faculty of Medical Sciences Newcastle University, Newcastle, UK
| | - Helen Tuppen
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Eric Fitton
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Doug Turnbull
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Amy E Vincent
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.
- NIHR Biomedical Research Centre Research Centre, Translational and Clinical Research, Faculty of Medical Sciences Newcastle University, Newcastle, UK.
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research, Faculty of Medical Sciences Newcastle University, Newcastle, UK.
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17
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Urbisz AZ, Schmelz RM, Małota K, Chajec Ł, Świątek P. Conservative character of the germ-line cyst organization within enchytraeids (Annelida: Clitellata) ovary - New proofs based on two Achaeta species. Micron 2025; 188:103732. [PMID: 39547002 DOI: 10.1016/j.micron.2024.103732] [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: 07/19/2024] [Revised: 10/31/2024] [Accepted: 10/31/2024] [Indexed: 11/17/2024]
Abstract
Ovaries in a minute and mainly aquatic clitellates, collectively termed microdriles, are usually tiny paired gonads localized, depending on the family/subfamily, in segments VI, XI, XII, or XIII. Sometimes, two pairs of ovaries are present in consecutive segments, or ovaries are unpaired. Usually, accumulating yolk (vitellogenic) oocytes detach from ovaries and float in the coelom cavity. This study presents the microscopical analyses of unpaired ovaries found in two representatives of the genus Achaeta (family Enchytraeidae). The ovary is an inconspicuous organ composed of germ-line cysts uniting early meiotic cells. Cysts comprise 16 synchronously developing cells interconnected via cytoplasmic bridges to the central cytoplasmic mass, termed cytophore. Each interconnected cell has one bridge connecting it to the cytophore. Clustering germ cells are enveloped by elongated somatic cells. The developmental synchrony within cysts is lost when one cell per cyst forms prominent microvilli, gather vast amounts of nutrients (yolk), and becomes an oocyte. The remaining 15 cells do not form microvilli, grow slowly, and are regarded as nurse cells that supply the oocyte with organelles and probably macromolecules. Such cysts detach from the ovary and float freely in the segmental cavity. Nurse cells and vitellogenic oocyte are still connected to the ball-like cytophore. Vitellogenic oocytes gather vast amounts of reserve material, mainly protein spheres. Finally, oocytes lose contact with the cytophore, and nurse cells no longer accompany them. The ovary organization and oogenesis scenario observed in this study are broadly similar to that described for other enchytraeid species, such as Enchytraeus albidus and Grania postclitellochaeta, and have been classified as the "Enchytraeus" type of ovary. The obtained results show that despite the unpaired nature of the Achaeta ovary and some differences in ovary morphology and oogenesis between different enchytraeid taxa, the ovaries of these clitellates are consistently composed of 16-celled germ-line cysts equipped with cytophore. Moreover, the presence of cysts equipped with cytophore in the ovaries of the studied Achaeta specimens provides the subsequent evidence that the formation of such germ-line cysts is a conserved aspect of oogenesis within the Clitellata. This consistency in the ovarian and oogenic patterns underscores the evolutionary conservation of these reproductive traits within the Enchytraeidae and clitellate annelids.
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Affiliation(s)
- Anna Z Urbisz
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, Katowice 40-007, Poland.
| | | | - Karol Małota
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, Katowice 40-007, Poland
| | - Łukasz Chajec
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, Katowice 40-007, Poland
| | - Piotr Świątek
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, Katowice 40-007, Poland
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18
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Last MGF, Abendstein L, Voortman LM, Sharp TH. Streamlining segmentation of cryo-electron tomography datasets with Ais. eLife 2024; 13:RP98552. [PMID: 39704648 DOI: 10.7554/elife.98552] [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: 12/21/2024] Open
Abstract
Segmentation is a critical data processing step in many applications of cryo-electron tomography. Downstream analyses, such as subtomogram averaging, are often based on segmentation results, and are thus critically dependent on the availability of open-source software for accurate as well as high-throughput tomogram segmentation. There is a need for more user-friendly, flexible, and comprehensive segmentation software that offers an insightful overview of all steps involved in preparing automated segmentations. Here, we present Ais: a dedicated tomogram segmentation package that is geared towards both high performance and accessibility, available on GitHub. In this report, we demonstrate two common processing steps that can be greatly accelerated with Ais: particle picking for subtomogram averaging, and generating many-feature segmentations of cellular architecture based on in situ tomography data. Featuring comprehensive annotation, segmentation, and rendering functionality, as well as an open repository for trained models at aiscryoet.org, we hope that Ais will help accelerate research and dissemination of data involving cryoET.
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Affiliation(s)
- Mart G F Last
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Leoni Abendstein
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Lenard M Voortman
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
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19
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Mladjenovic SM, Chandok IS, Darbandi A, Nguyen LNM, Stordy B, Zhen M, Chan WCW. 3D electron microscopy for analyzing nanoparticles in the tumor endothelium. Proc Natl Acad Sci U S A 2024; 121:e2406331121. [PMID: 39665759 DOI: 10.1073/pnas.2406331121] [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: 03/31/2024] [Accepted: 10/10/2024] [Indexed: 12/13/2024] Open
Abstract
Delivering medical agents to diseased tissues has been challenging, leading researchers to study the in vivo transport process in the body for improving delivery. Many imaging techniques exist for mapping the distribution of medical agent-carrying nanoparticles in tissues, but they cannot capture the three-dimensional context of tissues with single nanoparticle resolution. Here, we developed 3DEM-NPD, a three-dimensional electron microscopy (3D EM) machine learning strategy to image and map single nanoparticle distributions (NPD) in tissues. 3DEM-NPD provides unbiased visualization and quantification of individual nanoparticles within organs. We applied this technique to quantify nanoparticle transport through tumor blood vessel endothelial cells. We measured the cell diameter, surface area, and volume and found that traditional 2D EM cannot accurately measure these features. We used machine learning to locate over 550,000 nanoparticles in less than 3 h with an accuracy of over 82%. The 3DEM-NPD method allowed us to establish a metric to quantify nanoparticle transport at the single nanoparticle level and to quantify the morphological features of ~2,800 vesicles. We find that on average there are only 2.4 nanoparticles per vesicle with a theoretical maximum of 158 nanoparticles per vesicle (~66x increase). These surprising results suggest the need to increase vesicle encapsulation efficiency for improved transport and they provide a benchmark for increasing nanoparticle transport and delivery. This technique may provide unique insights into the interactions between medical agents, drug carriers, emerging materials, and cells at the single-nanoparticle level throughout tissues.
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Affiliation(s)
- Stefan M Mladjenovic
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Ishaan S Chandok
- Department of Physics, Harvard University, Cambridge, MA 02138
- Center for Brain Science, Harvard University, Cambridge, MA 02138
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5P 1X5
| | - Ali Darbandi
- Nanoscale Biomedical Imaging Facility, Hospital for Sick Children, Toronto, ON M5G1H3, Canada
| | - Luan N M Nguyen
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Benjamin Stordy
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Mei Zhen
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5P 1X5
| | - Warren C W Chan
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
- School of Chemistry, Chemical Engineering, and Biotechnology, Nanyang Technological University, 637371, Singapore
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20
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Rappe A, Vihinen HA, Suomi F, Hassinen AJ, Ehsan H, Jokitalo ES, McWilliams TG. Longitudinal autophagy profiling of the mammalian brain reveals sustained mitophagy throughout healthy aging. EMBO J 2024; 43:6199-6231. [PMID: 39367235 PMCID: PMC11612485 DOI: 10.1038/s44318-024-00241-y] [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: 11/17/2023] [Revised: 07/24/2024] [Accepted: 08/16/2024] [Indexed: 10/06/2024] Open
Abstract
Mitophagy neutralizes mitochondrial damage, thereby preventing cellular dysfunction and apoptosis. Defects in mitophagy have been strongly implicated in age-related neurodegenerative disorders such as Parkinson's and Alzheimer's disease. While mitophagy decreases throughout the lifespan of short-lived model organisms, it remains unknown whether such a decline occurs in the aging mammalian brain-a question of fundamental importance for understanding cell type- and region-specific susceptibility to neurodegeneration. Here, we define the longitudinal dynamics of basal mitophagy and macroautophagy across neuronal and non-neuronal cell types within the intact aging mouse brain in vivo. Quantitative profiling of reporter mouse cohorts from young to geriatric ages reveals cell- and tissue-specific alterations in mitophagy and macroautophagy between distinct subregions and cell populations, including dopaminergic neurons, cerebellar Purkinje cells, astrocytes, microglia and interneurons. We also find that healthy aging is hallmarked by the dynamic accumulation of differentially acidified lysosomes in several neural cell subsets. Our findings argue against any widespread age-related decline in mitophagic activity, instead demonstrating dynamic fluctuations in mitophagy across the aging trajectory, with strong implications for ongoing theragnostic development.
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Affiliation(s)
- Anna Rappe
- Translational Stem Cell Biology and Metabolism Program, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Haartmaninkatu 8, Helsinki, 00290, Finland
| | - Helena A Vihinen
- Electron Microscopy Unit (EMBI), Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Viikinkaari 9, Helsinki, 00790, Finland
| | - Fumi Suomi
- Translational Stem Cell Biology and Metabolism Program, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Haartmaninkatu 8, Helsinki, 00290, Finland
| | - Antti J Hassinen
- High Content Imaging and Analysis Unit (FIMM-HCA), Institute for Molecular Medicine, Helsinki Institute of Life Science, University of Helsinki, Tukholmankatu 8, Helsinki, 00290, Finland
| | - Homa Ehsan
- Translational Stem Cell Biology and Metabolism Program, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Haartmaninkatu 8, Helsinki, 00290, Finland
| | - Eija S Jokitalo
- Electron Microscopy Unit (EMBI), Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Viikinkaari 9, Helsinki, 00790, Finland
| | - Thomas G McWilliams
- Translational Stem Cell Biology and Metabolism Program, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Haartmaninkatu 8, Helsinki, 00290, Finland.
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, Helsinki, 00290, Finland.
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21
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Perdok A, Van Acker ZP, Vrancx C, Sannerud R, Vorsters I, Verrengia A, Callaerts-Végh Z, Creemers E, Gutiérrez Fernández S, D'hauw B, Serneels L, Wierda K, Chávez-Gutiérrez L, Annaert W. Altered expression of Presenilin2 impacts endolysosomal homeostasis and synapse function in Alzheimer's disease-relevant brain circuits. Nat Commun 2024; 15:10412. [PMID: 39613768 PMCID: PMC11607342 DOI: 10.1038/s41467-024-54777-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 11/21/2024] [Indexed: 12/01/2024] Open
Abstract
Rare mutations in the gene encoding presenilin2 (PSEN2) are known to cause familial Alzheimer's disease (FAD). Here, we explored how altered PSEN2 expression impacts on the amyloidosis, endolysosomal abnormalities, and synaptic dysfunction observed in female APP knock-in mice. We demonstrate that PSEN2 knockout (KO) as well as the FAD-associated N141IKI mutant accelerate AD-related pathologies in female mice. Both models showed significant deficits in working memory that linked to elevated PSEN2 expression in the hippocampal CA3 region. The mossy fiber circuit of APPxPSEN2KO and APPxFADPSEN2 mice had smaller pre-synaptic compartments, distinct changes in synaptic vesicle populations and significantly impaired long term potentiation compared to APPKI mice. At the cellular level, altered PSEN2 expression resulted in endolysosomal defects and lowered surface expression of synaptic proteins. As PSEN2/γ-secretase is restricted to late endosomes/lysosomes, we propose PSEN2 impacts endolysosomal homeostasis, affecting synaptic signaling in AD-relevant vulnerable brain circuits; which could explain how mutant PSEN2 accelerates AD pathogenesis.
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Affiliation(s)
- Anika Perdok
- Laboratory for Membrane Trafficking, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49box 602, Leuven, Belgium
| | - Zoë P Van Acker
- Laboratory for Membrane Trafficking, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49box 602, Leuven, Belgium
| | - Céline Vrancx
- Laboratory for Membrane Trafficking, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49box 602, Leuven, Belgium
| | - Ragna Sannerud
- Laboratory for Membrane Trafficking, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49box 602, Leuven, Belgium
| | - Inge Vorsters
- Laboratory for Membrane Trafficking, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49box 602, Leuven, Belgium
| | - Assunta Verrengia
- Laboratory for Membrane Trafficking, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Herestraat 49box 602, Leuven, Belgium
| | - Zsuzsanna Callaerts-Végh
- mINT Animal Behavior Facility, Faculty of Psychology, KU Leuven, Tiensestraat 102, Leuven, Belgium
| | - Eline Creemers
- Electrophysiology Expertise Unit, VIB-Center for Brain and Disease Research, Leuven, Belgium
| | - Sara Gutiérrez Fernández
- Department of Neurosciences, KU Leuven, Herestraat 49box 602, Leuven, Belgium
- Laboratory of Proteolytic Mechanisms mediating Neurodegeneration, Leuven, Belgium
| | - Britt D'hauw
- Electrophysiology Expertise Unit, VIB-Center for Brain and Disease Research, Leuven, Belgium
| | - Lutgarde Serneels
- Department of Neurosciences, KU Leuven, Herestraat 49box 602, Leuven, Belgium
- Mouse Expertise Unit, VIB-Center for Brain and Disease Research, Leuven, Belgium
| | - Keimpe Wierda
- Electrophysiology Expertise Unit, VIB-Center for Brain and Disease Research, Leuven, Belgium
| | - Lucía Chávez-Gutiérrez
- Department of Neurosciences, KU Leuven, Herestraat 49box 602, Leuven, Belgium
- Laboratory of Proteolytic Mechanisms mediating Neurodegeneration, Leuven, Belgium
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB Center for Brain and Disease Research, Leuven, Belgium.
- Department of Neurosciences, KU Leuven, Herestraat 49box 602, Leuven, Belgium.
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22
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Takahashi M, Yamamoto S, Yamamoto S, Okubo A, Nakagawa Y, Kuwahara K, Matsusaka T, Fukuma S, Yamamoto M, Matsuda M, Yanagita M. ATP dynamics as a predictor of future podocyte structure and function after acute ischemic kidney injury in female mice. Nat Commun 2024; 15:9977. [PMID: 39578451 PMCID: PMC11584722 DOI: 10.1038/s41467-024-54222-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 11/04/2024] [Indexed: 11/24/2024] Open
Abstract
Acute kidney injury (AKI), typically caused by ischemia, is a common clinical complication with a poor prognosis. Although proteinuria is an important prognostic indicator of AKI, the underlying causal mechanism remains unclear. In vitro studies suggest that podocytes have high ATP demands to maintain their structure and function, however, analyzing their ATP dynamics in living kidneys has been technically challenging. Here, using intravital imaging to visualize a FRET-based ATP biosensor expressed systemically in female mice due to their suitability for glomerular imaging, we monitor the in vivo ATP dynamics in podocytes during ischemia reperfusion injury. ATP levels decrease during ischemia, but recover after reperfusion in podocytes, exhibiting better recovery than in glomerular endothelial cells. However, prolonged ischemia results in insufficient ATP recovery in podocytes, which is inversely correlated with mitochondrial fragmentation and foot process effacement during the chronic phase. Furthermore, preventing mitochondrial fission via pharmacological inhibition ameliorates podocyte injury in vitro, ex vivo, and in vivo. Thus, these findings provide several insights into how ATP depletion and mitochondrial fragmentation contribute to podocyte injury after ischemic AKI and could potentially be therapeutic targets.
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Affiliation(s)
- Masahiro Takahashi
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shinya Yamamoto
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shigenori Yamamoto
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Akihiro Okubo
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuaki Nakagawa
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koichiro Kuwahara
- Department of Cardiovascular Medicine, Shinshu University School of Medicine, Matsumoto, Japan
| | - Taiji Matsusaka
- Institute of Medical Science and Department of Physiology, Tokai University School of Medicine, Isehara, Japan
| | - Shingo Fukuma
- Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Epidemiology Infectious Disease Control and Prevention, Hiroshima University Graduate school of Biomedical and Health Sciences, Hiroshima, Japan
| | - Masamichi Yamamoto
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- National Cerebral and Cardiovascular Center Reaesrch Institute, Osaka, Japan
| | - Michiyuki Matsuda
- Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan
| | - Motoko Yanagita
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan.
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23
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García Casas P, Rossini M, Påvénius L, Saeed M, Arnst N, Sonda S, Fernandes T, D'Arsiè I, Bruzzone M, Berno V, Raimondi A, Sassano ML, Naia L, Barbieri E, Sigismund S, Agostinis P, Sturlese M, Niemeyer BA, Brismar H, Ankarcrona M, Gautier A, Pizzo P, Filadi R. Simultaneous detection of membrane contact dynamics and associated Ca 2+ signals by reversible chemogenetic reporters. Nat Commun 2024; 15:9775. [PMID: 39532847 PMCID: PMC11557831 DOI: 10.1038/s41467-024-52985-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 09/25/2024] [Indexed: 11/16/2024] Open
Abstract
Membrane contact sites (MCSs) are hubs allowing various cell organelles to coordinate their activities. The dynamic nature of these sites and their small size hinder analysis by current imaging techniques. To overcome these limitations, we here design a series of reversible chemogenetic reporters incorporating improved, low-affinity variants of splitFAST, and study the dynamics of different MCSs at high spatiotemporal resolution, both in vitro and in vivo. We demonstrate that these versatile reporters suit different experimental setups well, allowing one to address challenging biological questions. Using these probes, we identify a pathway in which calcium (Ca2+) signalling dynamically regulates endoplasmic reticulum-mitochondria juxtaposition, characterizing the underlying mechanism. Finally, by integrating Ca2+-sensing capabilities into the splitFAST technology, we introduce PRINCESS (PRobe for INterorganelle Ca2+-Exchange Sites based on SplitFAST), a class of reporters to simultaneously detect MCSs and measure the associated Ca2+ dynamics using a single biosensor.
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Affiliation(s)
- Paloma García Casas
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- Department of Biochemistry, Molecular Biology and Physiology, Faculty of Medicine, Unidad de Excelencia Instituto de Biología y Genética Molecular (IBGM), University of Valladolid and CSIC, Valladolid, Spain
| | - Michela Rossini
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- Institute of Neuroscience, National Research Council (CNR), Padua, Italy
| | - Linnea Påvénius
- Science for Life Laboratory,, Karolinska Institutet, Stockholm, Sweden
| | - Mezida Saeed
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
| | - Nikita Arnst
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Sonia Sonda
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- Institute of Neuroscience, National Research Council (CNR), Padua, Italy
| | - Tânia Fernandes
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Irene D'Arsiè
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- Institute of Neuroscience, National Research Council (CNR), Padua, Italy
| | - Matteo Bruzzone
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Valeria Berno
- ALEMBIC, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Raimondi
- ALEMBIC, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, CH-6500, Bellinzona, Switzerland
| | - Maria Livia Sassano
- Cell Death Research and Therapy lab, Department of Cellular and Molecular Medicine, and Center for Cancer Biology-VIB, KU Leuven, Leuven, Belgium
| | - Luana Naia
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden
| | | | - Sara Sigismund
- IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hematology-Oncology, Università degli Studi di Milano, Milan, Italy
| | - Patrizia Agostinis
- Cell Death Research and Therapy lab, Department of Cellular and Molecular Medicine, and Center for Cancer Biology-VIB, KU Leuven, Leuven, Belgium
| | - Mattia Sturlese
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | | | - Hjalmar Brismar
- Science for Life Laboratory,, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
| | - Maria Ankarcrona
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden
| | - Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
| | - Paola Pizzo
- Department of Biomedical Sciences, University of Padua, Padua, Italy.
- Institute of Neuroscience, National Research Council (CNR), Padua, Italy.
- Centro Studi per la Neurodegenerazione (CESNE), University of Padua, Padua, Italy.
| | - Riccardo Filadi
- Department of Biomedical Sciences, University of Padua, Padua, Italy.
- Institute of Neuroscience, National Research Council (CNR), Padua, Italy.
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24
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Jerlström-Hultqvist J, Gallot-Lavallée L, Salas-Leiva DE, Curtis BA, Záhonová K, Čepička I, Stairs CW, Pipaliya S, Dacks JB, Archibald JM, Roger AJ. A unique symbiosome in an anaerobic single-celled eukaryote. Nat Commun 2024; 15:9726. [PMID: 39521804 PMCID: PMC11550330 DOI: 10.1038/s41467-024-54102-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 10/31/2024] [Indexed: 11/16/2024] Open
Abstract
Symbiotic relationships between eukaryotes and prokaryotes played pivotal roles in the evolution of life and drove the emergence of specialized symbiotic structures in animals, plants and fungi. The host-evolved symbiotic structures of microbial eukaryotes - the vast majority of such hosts in nature - remain largely unstudied. Here we describe highly structured symbiosomes within three free-living anaerobic protists (Anaeramoeba spp.). We dissect this symbiosis using complete genome sequencing and transcriptomics of host and symbiont cells coupled with fluorescence in situ hybridization, and 3D reconstruction using focused-ion-beam scanning electron microscopy. The emergence of the symbiosome is underpinned by expansion of gene families encoding regulators of membrane trafficking and phagosomal maturation and extensive bacteria-to-eukaryote lateral transfer. The symbionts reside deep within a symbiosomal membrane network that enables metabolic syntrophy by precisely positioning sulfate-reducing bacteria alongside host hydrogenosomes. Importantly, the symbionts maintain connections to the Anaeramoeba plasma membrane, blurring traditional boundaries between ecto- and endosymbiosis.
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Affiliation(s)
- Jon Jerlström-Hultqvist
- Department of Cell and Molecular Biology, Uppsala Universitet, Uppsala, Sweden.
- Institute for Comparative Genomics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada.
| | - Lucie Gallot-Lavallée
- Institute for Comparative Genomics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Dayana E Salas-Leiva
- Institute for Comparative Genomics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Bruce A Curtis
- Institute for Comparative Genomics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Kristína Záhonová
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, and Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czechia
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
- Life Science Research Centre, Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | | | - Shweta Pipaliya
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, and Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, and Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czechia
- Centre for Life's Origin and Evolution, Department of Genetics, Evolution, & Environment, University College, London, UK
| | - John M Archibald
- Institute for Comparative Genomics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Andrew J Roger
- Institute for Comparative Genomics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada.
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25
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Esposito A, Seri T, Breccia M, Indrigo M, De Rocco G, Nuzzolillo F, Denti V, Pappacena F, Tartaglione G, Serrao S, Paglia G, Murru L, de Pretis S, Cioni JM, Landsberger N, Guarnieri FC, Palmieri M. Unraveling autophagic imbalances and therapeutic insights in Mecp2-deficient models. EMBO Mol Med 2024; 16:2795-2826. [PMID: 39402139 PMCID: PMC11555085 DOI: 10.1038/s44321-024-00151-w] [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: 12/22/2023] [Revised: 09/16/2024] [Accepted: 09/27/2024] [Indexed: 11/13/2024] Open
Abstract
Loss-of-function mutations in MECP2 are associated to Rett syndrome (RTT), a severe neurodevelopmental disease. Mainly working as a transcriptional regulator, MeCP2 absence leads to gene expression perturbations resulting in deficits of synaptic function and neuronal activity. In addition, RTT patients and mouse models suffer from a complex metabolic syndrome, suggesting that related cellular pathways might contribute to neuropathogenesis. Along this line, autophagy is critical in sustaining developing neuron homeostasis by breaking down dysfunctional proteins, lipids, and organelles.Here, we investigated the autophagic pathway in RTT and found reduced content of autophagic vacuoles in Mecp2 knock-out neurons. This correlates with defective lipidation of LC3B, probably caused by a deficiency of the autophagic membrane lipid phosphatidylethanolamine. The administration of the autophagy inducer trehalose recovers LC3B lipidation, autophagosomes content in knock-out neurons, and ameliorates their morphology, neuronal activity and synaptic ultrastructure. Moreover, we provide evidence for attenuation of motor and exploratory impairment in Mecp2 knock-out mice upon trehalose administration. Overall, our findings open new perspectives for neurodevelopmental disorders therapies based on the concept of autophagy modulation.
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Affiliation(s)
- Alessandro Esposito
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy.
| | - Tommaso Seri
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Martina Breccia
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy
| | - Marzia Indrigo
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giuseppina De Rocco
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy
| | | | - Vanna Denti
- School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Francesca Pappacena
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Gaia Tartaglione
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Simone Serrao
- School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Giuseppe Paglia
- School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Luca Murru
- CNR Institute of Neuroscience, Vedano al Lambro, Italy
| | - Stefano de Pretis
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Jean-Michel Cioni
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Nicoletta Landsberger
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy
| | - Fabrizia Claudia Guarnieri
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy.
- CNR Institute of Neuroscience, Vedano al Lambro, Italy.
| | - Michela Palmieri
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Vita-Salute San Raffaele University, Milan, Italy.
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26
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Müller A, Klena N, Pang S, Garcia LEG, Topcheva O, Aurrecoechea Duran S, Sulaymankhil D, Seliskar M, Mziaut H, Schöniger E, Friedland D, Kipke N, Kretschmar S, Münster C, Weitz J, Distler M, Kurth T, Schmidt D, Hess HF, Xu CS, Pigino G, Solimena M. Structure, interaction and nervous connectivity of beta cell primary cilia. Nat Commun 2024; 15:9168. [PMID: 39448638 PMCID: PMC11502866 DOI: 10.1038/s41467-024-53348-5] [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: 12/21/2023] [Accepted: 10/04/2024] [Indexed: 10/26/2024] Open
Abstract
Primary cilia are sensory organelles present in many cell types, partaking in various signaling processes. Primary cilia of pancreatic beta cells play pivotal roles in paracrine signaling and their dysfunction is linked to diabetes. Yet, the structural basis for their functions is unclear. We present three-dimensional reconstructions of beta cell primary cilia by electron and expansion microscopy. These cilia are spatially confined within deep ciliary pockets or narrow spaces between cells, lack motility components and display an unstructured axoneme organization. Furthermore, we observe a plethora of beta cell cilia-cilia and cilia-cell interactions with other islet and non-islet cells. Most remarkably, we have identified and characterized axo-ciliary synapses between beta cell cilia and the cholinergic islet innervation. These findings highlight the beta cell cilia's role in islet connectivity, pointing at their function in integrating islet intrinsic and extrinsic signals and contribute to understanding their significance in health and diabetes.
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Affiliation(s)
- Andreas Müller
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany.
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Munich, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany.
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany.
| | | | - Song Pang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Yale School of Medicine, New Haven, CT, USA
| | - Leticia Elizabeth Galicia Garcia
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Munich, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- DFG Cluster of Excellence "Physics of Life", TU Dresden, Dresden, Germany
| | - Oleksandra Topcheva
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Munich, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Solange Aurrecoechea Duran
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Munich, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Davud Sulaymankhil
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Munich, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Department of Chemical Engineering, Cooper Union, New York City, NY, USA
| | - Monika Seliskar
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Munich, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Hassan Mziaut
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Munich, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Eyke Schöniger
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Munich, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Daniela Friedland
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Munich, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Nicole Kipke
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Munich, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Susanne Kretschmar
- Center for Molecular and Cellular Bioengineering (CMCB), Technology Platform, Core Facility Electron Microscopy and Histology, TU Dresden, Dresden, Germany
| | - Carla Münster
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Munich, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Jürgen Weitz
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital Carl Gustav Carus, Medical Faculty, TU Dresden, Dresden, Germany
| | - Marius Distler
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital Carl Gustav Carus, Medical Faculty, TU Dresden, Dresden, Germany
| | - Thomas Kurth
- Center for Molecular and Cellular Bioengineering (CMCB), Technology Platform, Core Facility Electron Microscopy and Histology, TU Dresden, Dresden, Germany
| | - Deborah Schmidt
- HELMHOLTZ IMAGING, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Harald F Hess
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - C Shan Xu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
| | | | - Michele Solimena
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany.
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Munich, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany.
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany.
- DFG Cluster of Excellence "Physics of Life", TU Dresden, Dresden, Germany.
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27
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Lee J, Matuschewski K, van Dooren G, Maier AG, Rug M. Lipid droplet dynamics are essential for the development of the malaria parasite Plasmodium falciparum. J Cell Sci 2024; 137:jcs262162. [PMID: 38962997 DOI: 10.1242/jcs.262162] [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: 03/28/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024] Open
Abstract
Lipid droplets (LDs) are organelles that are central to lipid and energy homeostasis across all eukaryotes. In the malaria-causing parasite Plasmodium falciparum the roles of LDs in lipid acquisition from its host cells and their metabolism are poorly understood, despite the high demand for lipids in parasite membrane synthesis. We systematically characterised LD size, composition and dynamics across the disease-causing blood infection. Applying split fluorescence emission analysis and three-dimensional (3D) focused ion beam-scanning electron microscopy (FIB-SEM), we observed a decrease in LD size in late schizont stages. LD contraction likely signifies a switch from lipid accumulation to lipid utilisation in preparation for parasite egress from host red blood cells. We demonstrate connections between LDs and several parasite organelles, pointing to potential functional interactions. Chemical inhibition of triacylglyerol (TAG) synthesis or breakdown revealed essential LD functions for schizogony and in counteracting lipid toxicity. The dynamics of lipid synthesis, storage and utilisation in P. falciparum LDs might provide a target for new anti-malarial intervention strategies.
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Affiliation(s)
- Jiwon Lee
- Centre for Advanced Microscopy, The Australian National University, Canberra ACT, 2601, Australia
- Research School of Biology, The Australian National University, Canberra ACT, 2601, Australia
| | - Kai Matuschewski
- Molecular Parasitology, Humboldt University, 10099 Berlin, Germany
| | - Giel van Dooren
- Research School of Biology, The Australian National University, Canberra ACT, 2601, Australia
| | - Alexander G Maier
- Research School of Biology, The Australian National University, Canberra ACT, 2601, Australia
| | - Melanie Rug
- Centre for Advanced Microscopy, The Australian National University, Canberra ACT, 2601, Australia
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28
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Thomas CI, Ryan MA, McNabb MC, Kamasawa N, Scholl B. Astrocyte coverage of excitatory synapses correlates to measures of synapse structure and function in ferret primary visual cortex. Glia 2024; 72:1785-1800. [PMID: 38856149 PMCID: PMC11324397 DOI: 10.1002/glia.24582] [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: 12/08/2023] [Revised: 05/25/2024] [Accepted: 06/02/2024] [Indexed: 06/11/2024]
Abstract
Most excitatory synapses in the mammalian brain are contacted or ensheathed by astrocyte processes, forming tripartite synapses. Astrocytes are thought to be critical regulators of the structural and functional dynamics of synapses. While the degree of synaptic coverage by astrocytes is known to vary across brain regions and animal species, the reason for and implications of this variability remains unknown. Further, how astrocyte coverage of synapses relates to in vivo functional properties of individual synapses has not been investigated. Here, we characterized astrocyte coverage of synapses of pyramidal neurons in the ferret visual cortex and, using correlative light and electron microscopy, examined their relationship to synaptic strength and sensory-evoked Ca2+ activity. Nearly, all synapses were contacted by astrocytes, and most were contacted along the axon-spine interface. Structurally, we found that the degree of synaptic astrocyte coverage directly scaled with synapse size and postsynaptic density complexity. Functionally, we found that the amount of astrocyte coverage scaled with how selectively a synapse responds to a particular visual stimulus and, at least for the largest synapses, scaled with the reliability of visual stimuli to evoke postsynaptic Ca2+ events. Our study shows astrocyte coverage is highly correlated with structural metrics of synaptic strength of excitatory synapses in the visual cortex and demonstrates a previously unknown relationship between astrocyte coverage and reliable sensory activation.
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Affiliation(s)
- Connon I Thomas
- Electron Microscopy Core Facility, Max Planck Florida Institute for Neuroscience, Jupiter, Florida, USA
| | - Melissa A Ryan
- Electron Microscopy Core Facility, Max Planck Florida Institute for Neuroscience, Jupiter, Florida, USA
| | - Micaiah C McNabb
- Electron Microscopy Core Facility, Max Planck Florida Institute for Neuroscience, Jupiter, Florida, USA
| | - Naomi Kamasawa
- Electron Microscopy Core Facility, Max Planck Florida Institute for Neuroscience, Jupiter, Florida, USA
| | - Benjamin Scholl
- Department of Physiology and Biophysics, University of Colorado Denver, Aurora, Colorado, USA
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29
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Chechekhina E, Voloshin N, Kulebyakin K, Tyurin-Kuzmin P. Code-Free Machine Learning Solutions for Microscopy Image Processing: Deep Learning. Tissue Eng Part A 2024; 30:627-639. [PMID: 38556835 DOI: 10.1089/ten.tea.2024.0014] [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] [Indexed: 04/02/2024] Open
Abstract
In recent years, there has been a significant expansion in the realm of processing microscopy images, thanks to the advent of machine learning techniques. These techniques offer diverse applications for image processing. Currently, numerous methods are used for processing microscopy images in the field of biology, ranging from conventional machine learning algorithms to sophisticated deep learning artificial neural networks with millions of parameters. However, a comprehensive grasp of the intricacies of these methods usually necessitates proficiency in programming and advanced mathematics. In our comprehensive review, we explore various widely used deep learning approaches tailored for the processing of microscopy images. Our emphasis is on algorithms that have gained popularity in the field of biology and have been adapted to cater to users lacking programming expertise. In essence, our target audience comprises biologists interested in exploring the potential of deep learning algorithms, even without programming skills. Throughout the review, we elucidate each algorithm's fundamental concepts and capabilities without delving into mathematical and programming complexities. Crucially, all the highlighted algorithms are accessible on open platforms without requiring code, and we provide detailed descriptions and links within our review. It's essential to recognize that addressing each specific problem demands an individualized approach. Consequently, our focus is not on comparing algorithms but on delineating the problems they are adept at solving. In practical scenarios, researchers typically select multiple algorithms suited to their tasks and experimentally determine the most effective one. It is worth noting that microscopy extends beyond the realm of biology; its applications span diverse fields such as geology and material science. Although our review predominantly centers on biomedical applications, the algorithms and principles outlined here are equally applicable to other scientific domains. Furthermore, a number of the proposed solutions can be modified for use in entirely distinct computer vision cases.
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Affiliation(s)
- Elizaveta Chechekhina
- Department of Biochemistry and Regenerative Biomedicine, Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Nikita Voloshin
- Department of Biochemistry and Regenerative Biomedicine, Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Konstantin Kulebyakin
- Department of Biochemistry and Regenerative Biomedicine, Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Pyotr Tyurin-Kuzmin
- Department of Biochemistry and Regenerative Biomedicine, Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
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30
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Nguyen KT, Sathler AR, Estevez AG, Logan IE, Franco MC. ProDiVis: a method to normalize fluorescence signal localization in 3D specimens. Front Cell Dev Biol 2024; 12:1420161. [PMID: 39376633 PMCID: PMC11456528 DOI: 10.3389/fcell.2024.1420161] [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: 04/19/2024] [Accepted: 09/04/2024] [Indexed: 10/09/2024] Open
Abstract
A common problem in confocal microscopy is the decrease in intensity of excitation light and emission signal from fluorophores as they travel through 3D specimens, resulting in decreased signal detected as a function of depth. Here, we report a visualization program compatible with widely used fluorophores in cell biology to facilitate image interpretation of differential protein disposition in 3D specimens. Glioblastoma cell clusters were fluorescently labeled for mitochondrial complex I (COXI), P2X7 receptor (P2X7R), β-Actin, Ki-67, and DAPI. Each cell cluster was imaged using a laser scanning confocal microscope. We observed up to ∼70% loss in fluorescence signal across the depth in Z-stacks. This progressive underrepresentation of fluorescence intensity as the focal plane deepens hinders an accurate representation of signal location within a 3D structure. To address these challenges, we developed ProDiVis: a program that adjusts apparent fluorescent signals by normalizing one fluorescent signal to a reference signal at each focal plane. ProDiVis serves as a free and accessible, unbiased visualization tool to use in conjunction with fluorescence microscopy images and imaging software.
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Affiliation(s)
- Kyle T. Nguyen
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States
| | - Alexandre R. Sathler
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States
| | - Alvaro G. Estevez
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States
- Herbert Wertheim College of Medicine, Florida International University, Port St. Lucie, FL, United States
- Center for Translational Science, Florida International University, Port St. Lucie, FL, United States
| | - Isabelle E. Logan
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States
| | - Maria Clara Franco
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States
- Herbert Wertheim College of Medicine, Florida International University, Port St. Lucie, FL, United States
- Center for Translational Science, Florida International University, Port St. Lucie, FL, United States
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31
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Rubin S, Agrawal A, Seewald A, Lian MJ, Gottdenker O, Villoutreix P, Baule A, Stern T, Zelzer E. Limited column formation in the embryonic growth plate implies divergent growth mechanisms during pre- and postnatal bone development. eLife 2024; 13:e95289. [PMID: 39269144 PMCID: PMC11509684 DOI: 10.7554/elife.95289] [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: 12/13/2023] [Accepted: 09/09/2024] [Indexed: 09/15/2024] Open
Abstract
Chondrocyte columns, which are a hallmark of growth plate architecture, play a central role in bone elongation. Columns are formed by clonal expansion following rotation of the division plane, resulting in a stack of cells oriented parallel to the growth direction. In this work, we analyzed hundreds of Confetti multicolor clones in growth plates of mouse embryos using a pipeline comprising 3D imaging and algorithms for morphometric analysis. Surprisingly, analysis of the elevation angles between neighboring pairs of cells revealed that most cells did not display the typical stacking pattern associated with column formation, implying incomplete rotation of the division plane. Morphological analysis revealed that although embryonic clones were elongated, they formed clusters oriented perpendicular to the growth direction. Analysis of growth plates of postnatal mice revealed both complex columns, composed of ordered and disordered cell stacks, and small, disorganized clusters located in the outer edges. Finally, correlation between the temporal dynamics of the ratios between clusters and columns and between bone elongation and expansion suggests that clusters may promote expansion, whereas columns support elongation. Overall, our findings support the idea that modulations of division plane rotation of proliferating chondrocytes determines the formation of either clusters or columns, a multifunctional design that regulates morphogenesis throughout pre- and postnatal bone growth. Broadly, this work provides a new understanding of the cellular mechanisms underlying growth plate activity and bone elongation during development.
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Affiliation(s)
- Sarah Rubin
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
| | - Ankit Agrawal
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
- Würzburg Institute of Systems Immunology, Julius‐Maximilians‐Universität WürzburgWürzburgGermany
| | - Anne Seewald
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
| | - Meng-Jia Lian
- Department of Biologic and Materials & Prosthodontics, University of Michigan School of DentistryAnn ArborUnited States
| | - Olivia Gottdenker
- Department of Biologic and Materials & Prosthodontics, University of Michigan School of DentistryAnn ArborUnited States
| | - Paul Villoutreix
- Aix Marseille Univ, INSERM, MMG, UMR1251, Turing Center for Living SystemsMarseilleFrance
| | - Adrian Baule
- School of Mathematical Sciences, Queen Mary University of LondonLondonUnited Kingdom
| | - Tomer Stern
- Department of Biologic and Materials & Prosthodontics, University of Michigan School of DentistryAnn ArborUnited States
| | - Elazar Zelzer
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
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32
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Burke MJ, Batista VS, Davis CM. Similarity Metrics for Subcellular Analysis of FRET Microscopy Videos. J Phys Chem B 2024; 128:8344-8354. [PMID: 39186078 DOI: 10.1021/acs.jpcb.4c02859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Understanding the heterogeneity of molecular environments within cells is an outstanding challenge of great fundamental and technological interest. Cells are organized into specialized compartments, each with distinct functions. These compartments exhibit dynamic heterogeneity under high-resolution microscopy, which reflects fluctuations in molecular populations, concentrations, and spatial distributions. To enhance our comprehension of the spatial relationships among molecules within cells, it is crucial to analyze images of high-resolution microscopy by clustering individual pixels according to their visible spatial properties and their temporal evolution. Here, we evaluate the effectiveness of similarity metrics based on their ability to facilitate fast and accurate data analysis in time and space. We discuss the capability of these metrics to differentiate subcellular localization, kinetics, and structures of protein-RNA interactions in Forster resonance energy transfer (FRET) microscopy videos, illustrated by a practical example from recent literature. Our results suggest that using the correlation similarity metric to cluster pixels of high-resolution microscopy data should improve the analysis of high-dimensional microscopy data in a wide range of applications.
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Affiliation(s)
- Michael J Burke
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Caitlin M Davis
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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33
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Laundon D, Proudley E, Basford PJ, Katsamenis OL, Chatelet DS, Cleal JK, Gostling NJ, Chavatte-Palmer P, Lewis RM. Quantitative microCT imaging of a whole equine placenta and its blood vessel network. Placenta 2024; 154:216-219. [PMID: 39096863 DOI: 10.1016/j.placenta.2024.07.313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/23/2024] [Accepted: 07/30/2024] [Indexed: 08/05/2024]
Abstract
Placental structure is linked to function across morphological scales. In the placenta, changes to gross anatomy, such as surface area, volume, or blood vessel arrangement, are associated with suboptimal physiological outcomes. However, quantifying each of these metrics requires different laborious semi-quantitative methods. Here, we demonstrate how, with minimal sample preparation, whole-organ computed microtomography (microCT) can be used to calculate gross morphometry of the equine placenta and a range of additional metrics, including branching morphometry of placental vasculature, non-destructively from a single dataset. Our approach can be applied to quantify the gross structure of any large mammalian placenta.
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Affiliation(s)
- Davis Laundon
- The Institute of Developmental Sciences, Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK; Institute for Life Sciences, University of Southampton, University Rd, Highfield, Southampton, SO17 1BJ, UK.
| | - Ella Proudley
- The Institute of Developmental Sciences, Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Philip J Basford
- Institute for Life Sciences, University of Southampton, University Rd, Highfield, Southampton, SO17 1BJ, UK; School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, University Road, Southampton, SO17 1BJ, UK; μ-VIS X-Ray Imaging Centre, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Orestis L Katsamenis
- Institute for Life Sciences, University of Southampton, University Rd, Highfield, Southampton, SO17 1BJ, UK; μ-VIS X-Ray Imaging Centre, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - David S Chatelet
- Biomedical Imaging Unit, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Jane K Cleal
- The Institute of Developmental Sciences, Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK; Institute for Life Sciences, University of Southampton, University Rd, Highfield, Southampton, SO17 1BJ, UK
| | - Neil J Gostling
- Institute for Life Sciences, University of Southampton, University Rd, Highfield, Southampton, SO17 1BJ, UK; School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, University Rd, Highfield, Southampton, SO17 1BJ, UK
| | - Pascale Chavatte-Palmer
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France; Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Rohan M Lewis
- The Institute of Developmental Sciences, Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK; Institute for Life Sciences, University of Southampton, University Rd, Highfield, Southampton, SO17 1BJ, UK
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Iavarone F, Zaninello M, Perrone M, Monaco M, Barth E, Gaedke F, Pizzo MT, Di Lorenzo G, Desiderio V, Sommella E, Merciai F, Salviati E, Campiglia P, Luongo L, De Leonibus E, Rugarli E, Settembre C. Fam134c and Fam134b shape axonal endoplasmic reticulum architecture in vivo. EMBO Rep 2024; 25:3651-3677. [PMID: 39039299 PMCID: PMC11316074 DOI: 10.1038/s44319-024-00213-7] [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: 02/09/2024] [Revised: 06/27/2024] [Accepted: 07/03/2024] [Indexed: 07/24/2024] Open
Abstract
Endoplasmic reticulum (ER) remodeling is vital for cellular organization. ER-phagy, a selective autophagy targeting ER, plays an important role in maintaining ER morphology and function. The FAM134 protein family, including FAM134A, FAM134B, and FAM134C, mediates ER-phagy. While FAM134B mutations are linked to hereditary sensory and autonomic neuropathy in humans, the physiological role of the other FAM134 proteins remains unknown. To address this, we investigate the roles of FAM134 proteins using single and combined knockouts (KOs) in mice. Single KOs in young mice show no major phenotypes; however, combined Fam134b and Fam134c deletion (Fam134b/cdKO), but not the combination including Fam134a deletion, leads to rapid neuromuscular and somatosensory degeneration, resulting in premature death. Fam134b/cdKO mice show rapid loss of motor and sensory axons in the peripheral nervous system. Long axons from Fam134b/cdKO mice exhibit expanded tubular ER with a transverse ladder-like appearance, whereas no obvious abnormalities are present in cortical ER. Our study unveils the critical roles of FAM134C and FAM134B in the formation of tubular ER network in axons of both motor and sensory neurons.
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Affiliation(s)
| | - Marta Zaninello
- Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Michela Perrone
- Department of Experimental Medicine, Division of Pharmacology, University of Campania "L. Vanvitelli", Naples, Italy
| | | | - Esther Barth
- Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Felix Gaedke
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | | | | | - Vincenzo Desiderio
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Via L. Armanni 5, 80138, Naples, Italy
| | - Eduardo Sommella
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, Fisciano, SA, 84084, Italy
| | - Fabrizio Merciai
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, Fisciano, SA, 84084, Italy
| | - Emanuela Salviati
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, Fisciano, SA, 84084, Italy
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, Fisciano, SA, 84084, Italy
| | - Livio Luongo
- Department of Experimental Medicine, Division of Pharmacology, University of Campania "L. Vanvitelli", Naples, Italy
| | - Elvira De Leonibus
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.
- Institute of Biochemistry and Cell Biology, Monterotondo, Rome, Italy.
| | - Elena Rugarli
- Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany.
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany.
- Center for Molecular Medicine, University of Cologne, Cologne, Germany.
| | - Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.
- Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy.
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35
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Ikäheimo K, Leinonen S, Lankinen T, Lindahl M, Saarma M, Pirvola U. Stereocilia fusion pathology in the cochlear outer hair cells at the nanoscale level. J Physiol 2024; 602:3995-4025. [PMID: 39037943 DOI: 10.1113/jp286318] [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: 01/22/2024] [Accepted: 06/12/2024] [Indexed: 07/24/2024] Open
Abstract
The hair bundle of cochlear hair cells comprises specialized microvilli, the stereocilia, which fulfil the role of mechanotransduction. Genetic defects and environmental noise challenge the maintenance of hair bundle structure, critically contributing to age-related hearing loss. Stereocilia fusion is a major component of the hair bundle pathology in mature hair cells, but its role in hearing loss and its molecular basis are poorly understood. Here, we utilized super-resolution expansion microscopy to examine the molecular anatomy of outer hair cell stereocilia fusion in mouse models of age-related hearing loss, heightened endoplasmic reticulum stress and prolonged noise exposure. Prominent stereocilia fusion in our model of heightened endoplasmic reticulum stress, Manf (Mesencephalic astrocyte-derived neurotrophic factor)-inactivated mice in a background with Cadherin 23 missense mutation, impaired mechanotransduction and calcium balance in stereocilia. This was indicated by reduced FM1-43 dye uptake through the mechanotransduction channels, reduced neuroplastin/PMCA2 expression and increased expression of the calcium buffer oncomodulin inside stereocilia. Sparse BAIAP2L2 and myosin 7a expression was retained in the fused stereocilia but mislocalized away from their functional sites at the tips. These hair bundle abnormalities preceded cell soma degeneration, suggesting a sequela from stereociliary molecular perturbations to cell death signalling. In the age-related hearing loss and noise-exposure models, stereocilia fusion was more restricted within the bundles, yet both models exhibited oncomodulin upregulation at the fusion sites, implying perturbed calcium homeostasis. We conclude that stereocilia fusion is linked with the failure to maintain cellular proteostasis and with disturbances in stereociliary calcium balance. KEY POINTS: Stereocilia fusion is a hair cell pathology causing hearing loss. Inactivation of Manf, a component of the endoplasmic reticulum proteostasis machinery, has a cell-intrinsic mode of action in triggering outer hair cell stereocilia fusion and the death of these cells. The genetic background with Cadherin 23 missense mutation contributes to the high susceptibility of outer hair cells to stereocilia fusion, evidenced in Manf-inactivated mice and in the mouse models of early-onset hearing loss and noise exposure. Endoplasmic reticulum stress feeds to outer hair cell stereocilia bundle pathology and impairs the molecular anatomy of calcium regulation. The maintenance of the outer hair cell stereocilia bundle cohesion is challenged by intrinsic and extrinsic stressors, and understanding the underlying mechanisms will probably benefit the development of interventions to promote hearing health.
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Affiliation(s)
- Kuu Ikäheimo
- Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Saija Leinonen
- Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Tuuli Lankinen
- Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Maria Lindahl
- Institute of Biotechnology, HILIFE Unit, University of Helsinki, Helsinki, Finland
| | - Mart Saarma
- Institute of Biotechnology, HILIFE Unit, University of Helsinki, Helsinki, Finland
| | - Ulla Pirvola
- Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
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36
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Laundon D, Lane T, Katsamenis OL, Norman J, Brewer L, Harris SE, Basford PJ, Shotton J, Free D, Constable-Dakeyne G, Gostling NJ, Chavatte-Palmer P, Lewis RM. Correlative three-dimensional X-ray histology (3D-XRH) as a tool for quantifying mammalian placental structure. Placenta 2024:S0143-4004(24)00607-6. [PMID: 39097490 DOI: 10.1016/j.placenta.2024.07.312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 07/15/2024] [Accepted: 07/30/2024] [Indexed: 08/05/2024]
Abstract
Mammalian placentas exhibit unparalleled structural diversity, despite sharing a common ancestor and principal functions. The bulk of structural studies in placental research has used two-dimensional (2D) histology sectioning, allowing significant advances in our understanding of mammalian placental structure. However, 2D histology sectioning may be limited if it does not provide accurate information of three-dimensional (3D) tissue architecture. Here, we propose correlative 3D X-ray histology (3D-XRH) as a tool with great potential for resolving mammalian placental structures. 3D-XRH involves scanning a formaldehyde-fixed, paraffin embedded (FFPE) tissue block with 3D X-ray microscopy (microCT) prior to histological sectioning to generate a 3D image volume of the embedded tissue piece. The subsequent 2D histology sections can then be correlated back into the microCT image volume to couple histology staining (or immunolabelling) with 3D tissue architecture. 3D-XRH is non-destructive and requires no additional sample preparation than standard FFPE histology sectioning, however the image volume provides 3D morphometric data and can be used to guide microtomy. As such, 3D-XRH introduces additional information to standard histological workflows with minimal effort or disruption. Using primary examples from porcine, bovine, equine, and canine placental samples, we demonstrate the application of 3D-XRH to quantifying placental structure as well as discussing the limitations and future directions of the methodology. The wealth of information derived from 2D histological sectioning in the biomedical, veterinary, and comparative reproductive sciences provides a rich foundation from which 3D-XRH can build on to advance the study of placental structure and function.
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Affiliation(s)
- Davis Laundon
- The Institute of Developmental Sciences, Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK; Institute for Life Sciences, University of Southampton, University Rd, Highfield, Southampton, SO17 1BJ, UK.
| | - Thomas Lane
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, University Rd, Highfield, Southampton, SO17 1BJ, UK
| | - Orestis L Katsamenis
- Institute for Life Sciences, University of Southampton, University Rd, Highfield, Southampton, SO17 1BJ, UK; μ-VIS X-Ray Imaging Centre, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Jeanette Norman
- Histochemistry Research Facility, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Lois Brewer
- School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, University Road, Southampton, SO17 1BJ, UK
| | - Shelley E Harris
- The Institute of Developmental Sciences, Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Philip J Basford
- Institute for Life Sciences, University of Southampton, University Rd, Highfield, Southampton, SO17 1BJ, UK; μ-VIS X-Ray Imaging Centre, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK; School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, University Road, Southampton, SO17 1BJ, UK
| | - Justine Shotton
- Marwell Wildlife, Thompson's Ln, Colden Common, Winchester, SO21 1JH, UK
| | - Danielle Free
- Marwell Wildlife, Thompson's Ln, Colden Common, Winchester, SO21 1JH, UK
| | | | - Neil J Gostling
- Institute for Life Sciences, University of Southampton, University Rd, Highfield, Southampton, SO17 1BJ, UK; School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, University Rd, Highfield, Southampton, SO17 1BJ, UK
| | - Pascale Chavatte-Palmer
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France; Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Rohan M Lewis
- The Institute of Developmental Sciences, Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK; Institute for Life Sciences, University of Southampton, University Rd, Highfield, Southampton, SO17 1BJ, UK
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37
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Wang L, Yang Z, Satoshi F, Prasanna X, Yan Z, Vihinen H, Chen Y, Zhao Y, He X, Bu Q, Li H, Zhao Y, Jiang L, Qin F, Dai Y, Zhang N, Qin M, Kuang W, Zhao Y, Jokitalo E, Vattulainen I, Kajander T, Zhao H, Cen X. Membrane remodeling by FAM92A1 during brain development regulates neuronal morphology, synaptic function, and cognition. Nat Commun 2024; 15:6209. [PMID: 39043703 PMCID: PMC11266426 DOI: 10.1038/s41467-024-50565-w] [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: 09/18/2023] [Accepted: 07/12/2024] [Indexed: 07/25/2024] Open
Abstract
The Bin/Amphiphysin/Rvs (BAR) domain protein FAM92A1 is a multifunctional protein engaged in regulating mitochondrial ultrastructure and ciliogenesis, but its physiological role in the brain remains unclear. Here, we show that FAM92A1 is expressed in neurons starting from embryonic development. FAM92A1 knockout in mice results in altered brain morphology and age-associated cognitive deficits, potentially due to neuronal degeneration and disrupted synaptic plasticity. Specifically, FAM92A1 deficiency impairs diverse neuronal membrane morphology, including the mitochondrial inner membrane, myelin sheath, and synapses, indicating its roles in membrane remodeling and maintenance. By determining the crystal structure of the FAM92A1 BAR domain, combined with atomistic molecular dynamics simulations, we uncover that FAM92A1 interacts with phosphoinositide- and cardiolipin-containing membranes to induce lipid-clustering and membrane curvature. Altogether, these findings reveal the physiological role of FAM92A1 in the brain, highlighting its impact on synaptic plasticity and neural function through the regulation of membrane remodeling and endocytic processes.
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Affiliation(s)
- Liang Wang
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Ziyun Yang
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Fudo Satoshi
- Helsinki Institute of Life Science - Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Xavier Prasanna
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Ziyi Yan
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Helena Vihinen
- Helsinki Institute of Life Science (HiLIFE) - Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Yaxing Chen
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Yue Zhao
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Xiumei He
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
- School of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Universities Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, 541004, China
| | - Qian Bu
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Hongchun Li
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Ying Zhao
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Linhong Jiang
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Feng Qin
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Yanping Dai
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Ni Zhang
- Mental Health Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Meng Qin
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Weihong Kuang
- Mental Health Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yinglan Zhao
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Eija Jokitalo
- Helsinki Institute of Life Science (HiLIFE) - Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Tommi Kajander
- Helsinki Institute of Life Science - Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hongxia Zhao
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.
- School of Life Sciences, Guangxi Normal University, Guilin, China.
- Guangxi Universities Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, 541004, China.
| | - Xiaobo Cen
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China.
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38
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Changela HG, Kebukawa Y, Petera L, Ferus M, Chatzitheodoridis E, Nejdl L, Nebel R, Protiva V, Krepelka P, Moravcova J, Holbova R, Hlavenkova Z, Samoril T, Bridges JC, Yamashita S, Takahashi Y, Yada T, Nakato A, Sobotkova K, Tesarova H, Zapotok D. The evolution of organic material on Asteroid 162173 Ryugu and its delivery to Earth. Nat Commun 2024; 15:6165. [PMID: 39039074 PMCID: PMC11263614 DOI: 10.1038/s41467-024-50004-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 06/27/2024] [Indexed: 07/24/2024] Open
Abstract
The recent return of samples from asteroid 162173 Ryugu provides a first insight into early Solar System prebiotic evolution from known planetary bodies. Ryugu's samples are CI chondrite-like, rich in water and organic material, and primarily composed of phyllosilicate. This phyllosilicate surrounds micron to submicron macromolecular organic particles known as insoluble organic matter. Using advanced microscopy techniques on Hayabusa-2 samples, we find that aqueous alteration on Ryugu produced organic particles richer in aromatics compared to less altered carbonaceous chondrites. This challenges the view that aromatic-rich organic matter formed pre-accretion. Additionally, widespread diffuse organic material occurs in phyllosilicate more aliphatic-, carboxylic-rich, and aromatic-poor than the discrete organic particles, likely preserving the soluble organic material. Some organic particles evolved to encapsulate phyllosilicate, indicating that aqueous alteration on Ryugu led to the containment of soluble organic matter within these particles. Earth therefore has been, and continues to be, delivered micron-sized polymeric organic objects containing biologically relevant molecules.
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Affiliation(s)
- H G Changela
- Department of Spectroscopy, J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czechia.
- Department of Earth & Planetary Sciences, University of New Mexico, Albuquerque, NM, USA.
| | - Y Kebukawa
- Department of Chemistry and Life Science, Yokohama National University, Yokohama, Japan
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, Tokyo, Japan
| | - L Petera
- Department of Spectroscopy, J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czechia
- Department of Inorganic Chemistry, Faculty of Science, Charles University, Prague, Czechia
| | - M Ferus
- Department of Spectroscopy, J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czechia
| | - E Chatzitheodoridis
- School of Mining and Metallurgical Engineering, National Technical University of Athens, Athens, Greece
- ESTEC, European Space Agency, Noordwijk, The Netherlands
| | - L Nejdl
- Department of Chemistry and Biochemistry, Mendel University, Brno, Czechia
| | - R Nebel
- Department of Spectroscopy, J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czechia
| | - V Protiva
- Department of Spectroscopy, J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czechia
| | - P Krepelka
- Central European Institute of Technology Masaryk University, Brno, Czechia
| | - J Moravcova
- Central European Institute of Technology Masaryk University, Brno, Czechia
| | - R Holbova
- Central European Institute of Technology Masaryk University, Brno, Czechia
| | - Z Hlavenkova
- Central European Institute of Technology Masaryk University, Brno, Czechia
| | - T Samoril
- Central European Institute of Technology, Brno University of Technology, Brno, Czechia
- TESCAN GROUP a.s., Brno, Czechia
| | - J C Bridges
- Space Park Leicester, School of Physics & Astronomy, University of Leicester, Leicester, UK
| | - S Yamashita
- Institute of Materials Structure Science, High-Energy Accelerator Research Organization, Ibaraki, Japan
| | - Y Takahashi
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo, Japan
| | - T Yada
- Astromaterials Science Research Group, Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Kanagawa, Japan
| | - A Nakato
- Astromaterials Science Research Group, Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Kanagawa, Japan
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Alharbi E, Rajaram A, Côté K, Farag M, Maleki F, Gao ZH, Maedler-Kron C, Marcus V, Fiset PO. A Deep Learning-Based Approach to Estimate Paneth Cell Granule Area in Celiac Disease. Arch Pathol Lab Med 2024; 148:828-835. [PMID: 37852171 DOI: 10.5858/arpa.2023-0074-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2023] [Indexed: 10/20/2023]
Abstract
CONTEXT.— Changes in Paneth cell numbers can be associated with chronic inflammatory diseases of the gastrointestinal tract. So far, no consensus has been achieved on the number of Paneth cells and their relevance to celiac disease (CD). OBJECTIVES.— To compare crypt and Paneth cell granule areas between patients with CD and those without CD (non-CD) using an artificial intelligence-based solution. DESIGN.— Hematoxylin-eosin-stained sections of duodenal biopsies from 349 patients at the McGill University Health Centre were analyzed. Of these, 185 had a history of CD and 164 were controls. Slides were digitized, and NoCodeSeg, a code-free workflow using open-source software (QuPath, DeepMIB), was implemented to train deep learning models to segment crypts and Paneth cell granules. The total area of the entire analyzed tissue, epithelium, crypts, and Paneth cell granules was documented for all slides, and comparisons were performed. RESULTS.— A mean intersection-over-union score of 88.76% and 91.30% was achieved for crypt areas and Paneth cell granule segmentations, respectively. On normalization to total tissue area, the crypt to total tissue area in CD was increased and the Paneth cell granule area to total tissue area decreased when compared to non-CD controls. CONCLUSIONS.— Crypt hyperplasia was confirmed in CD compared to non-CD controls. The area of Paneth cell granules, an indirect measure of Paneth cell function, decreased with increasing severity of CD. More importantly, our study analyzed complete hematoxylin-eosin slide sections using an efficient and easy to use coding-free artificial intelligence workflow.
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Affiliation(s)
- Ebtihal Alharbi
- From the Department of Pathology, McGill University, Montreal, Quebec, Canada (Alharbi, Rajaram, Côté, Farag, Gao, Maedler-Kron, Marcus, Fiset)
- Department of Pathology, Faculty of Medicine in Rabigh, King Abdulaziz University, Saudi Arabia (Alharbi)
| | - Ajay Rajaram
- From the Department of Pathology, McGill University, Montreal, Quebec, Canada (Alharbi, Rajaram, Côté, Farag, Gao, Maedler-Kron, Marcus, Fiset)
| | - Kevin Côté
- From the Department of Pathology, McGill University, Montreal, Quebec, Canada (Alharbi, Rajaram, Côté, Farag, Gao, Maedler-Kron, Marcus, Fiset)
| | - Mina Farag
- From the Department of Pathology, McGill University, Montreal, Quebec, Canada (Alharbi, Rajaram, Côté, Farag, Gao, Maedler-Kron, Marcus, Fiset)
| | - Farhad Maleki
- Augmented Intelligence & Precision Health Laboratory, Research Institute and Department of Radiology, McGill University Health Centre, Montreal, Quebec, Canada (Maleki)
- Department of Computer Science, University of Calgary, Calgary, Alberta, Canada (Maleki)
| | - Zu-Hua Gao
- From the Department of Pathology, McGill University, Montreal, Quebec, Canada (Alharbi, Rajaram, Côté, Farag, Gao, Maedler-Kron, Marcus, Fiset)
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada (Gao)
| | - Chelsea Maedler-Kron
- From the Department of Pathology, McGill University, Montreal, Quebec, Canada (Alharbi, Rajaram, Côté, Farag, Gao, Maedler-Kron, Marcus, Fiset)
- Research Institute of McGill University Health Center, Montreal, Quebec, Canada (Maedler-Kron, Fiset)
| | - Victoria Marcus
- From the Department of Pathology, McGill University, Montreal, Quebec, Canada (Alharbi, Rajaram, Côté, Farag, Gao, Maedler-Kron, Marcus, Fiset)
| | - Pierre Olivier Fiset
- From the Department of Pathology, McGill University, Montreal, Quebec, Canada (Alharbi, Rajaram, Côté, Farag, Gao, Maedler-Kron, Marcus, Fiset)
- Research Institute of McGill University Health Center, Montreal, Quebec, Canada (Maedler-Kron, Fiset)
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40
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Kolotuev I. Work smart, not hard: How array tomography can help increase the ultrastructure data output. J Microsc 2024; 295:42-60. [PMID: 37626455 DOI: 10.1111/jmi.13217] [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: 04/09/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023]
Abstract
Transmission electron microscopy has been essential for understanding cell biology for over six decades. Volume electron microscopy tools, such as serial block face and focused ion beam scanning electron microscopy acquisition, brought a new era to ultrastructure analysis. 'Array Tomography' (AT) refers to sequential image acquisition of resin-embedded sample sections on a large support (coverslip, glass slide, silicon wafers) for immunolabelling with multiple fluorescent labels, occasionally combined with ultrastructure observation. Subsequently, the term was applied to generating and imaging a series of sections to acquire a 3D representation of a structure using scanning electron microscopy (SEM). Although this is a valuable application, the potential of AT is to facilitate many tasks that are difficult or even impossible to obtain by Transmission Electron Microscopy (TEM). Due to the straightforward nature and versatility of AT sample preparation and image acquisition, the technique can be applied practically to any biological sample for selected sections or volume electron microscopy analysis. Furthermore, in addition to the benefits described here, AT is compatible with morphological analysis, multiplex immunolabelling, immune-gold labelling, and correlative light and electron microscopy workflow applicable for single cells, tissue and small organisms. This versatility makes AT attractive not only for basic research but as a diagnostic tool with a simplified routine.
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Affiliation(s)
- Irina Kolotuev
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
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Majstorović J, Kyslík J, Klak K, Maciuszek M, Chan JTH, Korytář T, Holzer AS. Erythrocytes of the common carp are immune sentinels that sense pathogen molecular patterns, engulf particles and secrete pro-inflammatory cytokines against bacterial infection. Front Immunol 2024; 15:1407237. [PMID: 38947329 PMCID: PMC11211254 DOI: 10.3389/fimmu.2024.1407237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024] Open
Abstract
Introduction Red blood cells (RBCs), also known as erythrocytes, are underestimated in their role in the immune system. In mammals, erythrocytes undergo maturation that involves the loss of nuclei, resulting in limited transcription and protein synthesis capabilities. However, the nucleated nature of non-mammalian RBCs is challenging this conventional understanding of RBCs. Notably, in bony fishes, research indicates that RBCs are not only susceptible to pathogen attacks but express immune receptors and effector molecules. However, given the abundance of RBCs and their interaction with every physiological system, we postulate that they act in surveillance as sentinels, rapid responders, and messengers. Methods We performed a series of in vitro experiments with Cyprinus carpio RBCs exposed to Aeromonas hydrophila, as well as in vivo laboratory infections using different concentrations of bacteria. Results qPCR revealed that RBCs express genes of several inflammatory cytokines. Using cyprinid-specific antibodies, we confirmed that RBCs secreted tumor necrosis factor alpha (TNFα) and interferon gamma (IFNγ). In contrast to these indirect immune mechanisms, we observed that RBCs produce reactive oxygen species and, through transmission electron and confocal microscopy, that RBCs can engulf particles. Finally, RBCs expressed and upregulated several putative toll-like receptors, including tlr4 and tlr9, in response to A. hydrophila infection in vivo. Discussion Overall, the RBC repertoire of pattern recognition receptors, their secretion of effector molecules, and their swift response make them immune sentinels capable of rapidly detecting and signaling the presence of foreign pathogens. By studying the interaction between a bacterium and erythrocytes, we provide novel insights into how the latter may contribute to overall innate and adaptive immune responses of teleost fishes.
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Affiliation(s)
- Jovana Majstorović
- Laboratory of Fish Protistology, Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Jiří Kyslík
- Laboratory of Fish Protistology, Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Katarzyna Klak
- Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Magdalena Maciuszek
- Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Justin T. H. Chan
- Laboratory of Fish Protistology, Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Fish Health Division, Veterinary University of Vienna, Vienna, Austria
| | - Tomáš Korytář
- Laboratory of Fish Protistology, Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Astrid S. Holzer
- Laboratory of Fish Protistology, Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Fish Health Division, Veterinary University of Vienna, Vienna, Austria
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Korelin K, Oostveen M, Wahbi W, Ianevski F, Cavalcante B, Turunen L, Belevich I, Al-Samadi A, Salo T. Evaluation of BH3 mimetics as a combination therapy with irradiation in head and neck squamous cell carcinoma. Biomed Pharmacother 2024; 175:116719. [PMID: 38749173 DOI: 10.1016/j.biopha.2024.116719] [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: 03/07/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 06/03/2024] Open
Abstract
INTRODUCTION Head and neck squamous cell carcinoma (HNSCC) is a common cancer with a five-year survival rate around 60%, indicating a need for new treatments. BH3 mimetics are small molecules that inhibit anti-apoptotic Bcl-2 family proteins, resulting in apoptosis induction. METHODS We performed a high-throughput screen using a Myogel matrix to identify the synergy between irradiation and the novel BH3 mimetics A-1155463, A-1331852, and navitoclax in 12 HNSCC cell lines, normal (NOF) and cancer-associated fibroblasts (CAF), and dysplastic keratinocytes (ODA). Next, we examined synergy in an apoptosis assay, followed by a clonogenic assay and a Myogel spheroid on selected HNSCC cell lines. Finally, we applied zebrafish larvae xenograft to validate the effects of navitoclax and A-1331852. RESULTS All three BH3 mimetics exhibited a strong synergy with irradiation in eight HNSCC cell lines and ODAs, but not in NOFs and CAFs. A-1155463 and A-1331852 induced apoptosis and reduced proliferation, and together with irradiation, significantly increased apoptosis and arrested proliferation. A-1331852 and navitoclax significantly decreased the clonogenicity compared with the control, and combination treatment led to a decreased clonogenicity compared with monotherapy or irradiation. However, unlike navitoclax or A-1155463, only A-1331852 significantly reduced cancer cell invasion. Furthermore, in spheroid and zebrafish, irradiation appeared ineffective and failed to significantly increase the drug effect. In the zebrafish, A-1331852 and navitoclax significantly reduced the tumor area and metastasis. CONCLUSIONS Our findings encourage the further preclinical investigation of BH3 mimetics, particularly A-1331852, as a single agent or combined with irradiation as a treatment for HNSCC.
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Affiliation(s)
- Katja Korelin
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki 00014, Finland; Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki 00014, Finland.
| | - Mayke Oostveen
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki 00014, Finland
| | - Wafa Wahbi
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki 00014, Finland; Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki 00014, Finland
| | - Filipp Ianevski
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00290, Finland
| | - Bruno Cavalcante
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki 00014, Finland; Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador 40296-710, Brazil; Department of Pathology and Forensic Medicine, School of Medicine, Federal University of Bahia, Salvador 40110-909, Brazil
| | - Laura Turunen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00290, Finland
| | - Ilya Belevich
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki 00014, Finland
| | - Ahmed Al-Samadi
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki 00014, Finland; Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki 00014, Finland; Institute of Dentistry, School of Medicine, Kuopio Campus, University of Eastern Finland, Kuopio, Finland
| | - Tuula Salo
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki 00014, Finland; Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki 00014, Finland; Cancer and Translational Medicine Research Unit, University of Oulu, Oulu 90014, Finland; Medical Research Center, Oulu University Hospital, Oulu 90220, Finland; Department of Pathology, Helsinki University Hospital (HUS), Helsinki 00029, Finland
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Matsumoto M, Matsushita K, Hane M, Wen C, Kurematsu C, Ota H, Bang Nguyen H, Quynh Thai T, Herranz-Pérez V, Sawada M, Fujimoto K, García-Verdugo JM, Kimura KD, Seki T, Sato C, Ohno N, Sawamoto K. Neuraminidase inhibition promotes the collective migration of neurons and recovery of brain function. EMBO Mol Med 2024; 16:1228-1253. [PMID: 38789599 PMCID: PMC11178813 DOI: 10.1038/s44321-024-00073-7] [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: 12/14/2023] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024] Open
Abstract
In the injured brain, new neurons produced from endogenous neural stem cells form chains and migrate to injured areas and contribute to the regeneration of lost neurons. However, this endogenous regenerative capacity of the brain has not yet been leveraged for the treatment of brain injury. Here, we show that in healthy brain chains of migrating new neurons maintain unexpectedly large non-adherent areas between neighboring cells, allowing for efficient migration. In instances of brain injury, neuraminidase reduces polysialic acid levels, which negatively regulates adhesion, leading to increased cell-cell adhesion and reduced migration efficiency. The administration of zanamivir, a neuraminidase inhibitor used for influenza treatment, promotes neuronal migration toward damaged regions, fosters neuronal regeneration, and facilitates functional recovery. Together, these findings shed light on a new mechanism governing efficient neuronal migration in the adult brain under physiological conditions, pinpoint the disruption of this mechanism during brain injury, and propose a promising therapeutic avenue for brain injury through drug repositioning.
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Affiliation(s)
- Mami Matsumoto
- Department of Developmental and Regenerative Neurobiology, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601, Japan
- Division of Neural Development and Regeneration, National Institute for Physiological Sciences, Okazaki, 444-8585, Japan
| | - Katsuyoshi Matsushita
- Department of Mathematical and Life Sciences, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Masaya Hane
- Bioscience and Biotechnology Center, Graduate School of Bioagricultural Sciences, and Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, 464-8601, Japan
| | - Chentao Wen
- Graduate School of Science, Nagoya City University, Nagoya, 467-8501, Japan
- Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, Kobe, 650-0047, Japan
| | - Chihiro Kurematsu
- Department of Developmental and Regenerative Neurobiology, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601, Japan
| | - Haruko Ota
- Department of Developmental and Regenerative Neurobiology, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601, Japan
- Department of Anesthesiology and Intensive Care Medicine, Graduate School of Medical Sciences, Nagoya City University, Nagoya, 467-8601, Japan
| | - Huy Bang Nguyen
- Section of Electron Microscopy, Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, 444-8787, Japan
- Department of Anatomy, Faculty of Medicine, University of Medicine and Pharmacy at Ho Chi Minh City (UMP), Ho Chi Minh City, 70000, Vietnam
| | - Truc Quynh Thai
- Section of Electron Microscopy, Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, 444-8787, Japan
- Department of Histology-Embryology-Genetics, Faculty of Basic Medical Sciences, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, 70000, Vietnam
| | - Vicente Herranz-Pérez
- Laboratory of Comparative Neurobiology, Cavanilles Institute, University of Valencia, CIBERNED-ISCIII, Valencia, 46980, Spain
- Department of Cell Biology, Functional Biology and Physical Anthropology, University of Valencia, Burjassot, 46100, Spain
| | - Masato Sawada
- Department of Developmental and Regenerative Neurobiology, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601, Japan
- Division of Neural Development and Regeneration, National Institute for Physiological Sciences, Okazaki, 444-8585, Japan
| | - Koichi Fujimoto
- Department of Mathematical and Life Sciences, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - José Manuel García-Verdugo
- Laboratory of Comparative Neurobiology, Cavanilles Institute, University of Valencia, CIBERNED-ISCIII, Valencia, 46980, Spain
| | - Koutarou D Kimura
- Graduate School of Science, Nagoya City University, Nagoya, 467-8501, Japan
| | - Tatsunori Seki
- Department of Histology and Neuroanatomy, Tokyo Medical University, Tokyo, 160-8402, Japan
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo, 160-8402, Japan
| | - Chihiro Sato
- Bioscience and Biotechnology Center, Graduate School of Bioagricultural Sciences, and Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, 464-8601, Japan
| | - Nobuhiko Ohno
- Department of Anatomy, Division of Histology and Cell Biology, Jichi Medical University, Shimotsuke, 329-0498, Japan
- Division of Ultrastructural Research, National Institute for Physiological Sciences, Okazaki, 444-8585, Japan
| | - Kazunobu Sawamoto
- Department of Developmental and Regenerative Neurobiology, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601, Japan.
- Division of Neural Development and Regeneration, National Institute for Physiological Sciences, Okazaki, 444-8585, Japan.
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Ikeda KN, Belevich I, Zelaya-Lainez L, Orel L, Füssl J, Gumulec J, Hellmich C, Jokitalo E, Raible F. Dynamic microvilli sculpt bristles at nanometric scale. Nat Commun 2024; 15:3733. [PMID: 38740737 PMCID: PMC11091046 DOI: 10.1038/s41467-024-48044-3] [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: 08/21/2023] [Accepted: 04/19/2024] [Indexed: 05/16/2024] Open
Abstract
Organisms generate shapes across size scales. Whereas patterning and morphogenesis of macroscopic tissues has been extensively studied, the principles underlying the formation of micrometric and submicrometric structures remain largely enigmatic. Individual cells of polychaete annelids, so-called chaetoblasts, are associated with the generation of chitinous bristles of highly stereotypic geometry. Here we show that bristle formation requires a chitin-producing enzyme specifically expressed in the chaetoblasts. Chaetoblasts exhibit dynamic cell surfaces with stereotypical patterns of actin-rich microvilli. These microvilli can be matched with internal and external structures of bristles reconstructed from serial block-face electron micrographs. Individual chitin teeth are deposited by microvilli in an extension-disassembly cycle resembling a biological 3D printer. Consistently, pharmacological interference with actin dynamics leads to defects in tooth formation. Our study reveals that both material and shape of bristles are encoded by the same cell, and that microvilli play a role in micro- to submicrometric sculpting of biomaterials.
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Affiliation(s)
- Kyojiro N Ikeda
- Max Perutz Labs; University of Vienna, 1030, Vienna, Austria.
| | - Ilya Belevich
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Luis Zelaya-Lainez
- Institute for Mechanics of Materials and Structures, TU Wien-Vienna University of Technology, Vienna, Austria
| | - Lukas Orel
- Max Perutz Labs; University of Vienna, 1030, Vienna, Austria
| | - Josef Füssl
- Institute for Mechanics of Materials and Structures, TU Wien-Vienna University of Technology, Vienna, Austria
| | - Jaromír Gumulec
- Department of Pathophysiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Christian Hellmich
- Institute for Mechanics of Materials and Structures, TU Wien-Vienna University of Technology, Vienna, Austria
| | - Eija Jokitalo
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Florian Raible
- Max Perutz Labs; University of Vienna, 1030, Vienna, Austria.
- Research Platform "Single-Cell Regulation of Stem Cells", University of Vienna, Vienna, Austria.
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Müller A, Schmidt D, Albrecht JP, Rieckert L, Otto M, Galicia Garcia LE, Fabig G, Solimena M, Weigert M. Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets. Nat Protoc 2024; 19:1436-1466. [PMID: 38424188 DOI: 10.1038/s41596-024-00957-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 11/24/2023] [Indexed: 03/02/2024]
Abstract
Volume electron microscopy is the method of choice for the in situ interrogation of cellular ultrastructure at the nanometer scale, and with the increase in large raw image datasets generated, improving computational strategies for image segmentation and spatial analysis is necessary. Here we describe a practical and annotation-efficient pipeline for organelle-specific segmentation, spatial analysis and visualization of large volume electron microscopy datasets using freely available, user-friendly software tools that can be run on a single standard workstation. The procedures are aimed at researchers in the life sciences with modest computational expertise, who use volume electron microscopy and need to generate three-dimensional (3D) segmentation labels for different types of cell organelles while minimizing manual annotation efforts, to analyze the spatial interactions between organelle instances and to visualize the 3D segmentation results. We provide detailed guidelines for choosing well-suited segmentation tools for specific cell organelles, and to bridge compatibility issues between freely available open-source tools, we distribute the critical steps as easily installable Album solutions for deep learning segmentation, spatial analysis and 3D rendering. Our detailed description can serve as a reference for similar projects requiring particular strategies for single- or multiple-organelle analysis, which can be achieved with computational resources commonly available to single-user setups.
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Affiliation(s)
- Andreas Müller
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany.
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany.
- German Center for Diabetes Research, Neuherberg, Germany.
| | - Deborah Schmidt
- HELMHOLTZ IMAGING, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.
| | - Jan Philipp Albrecht
- HELMHOLTZ IMAGING, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
- Humboldt-Universität zu Berlin, Faculty of Mathematics and Natural Sciences, Berlin, Germany
| | - Lucas Rieckert
- HELMHOLTZ IMAGING, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Maximilian Otto
- HELMHOLTZ IMAGING, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Leticia Elizabeth Galicia Garcia
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany
- German Center for Diabetes Research, Neuherberg, Germany
- DFG Cluster of Excellence 'Physics of Life', TU Dresden, Dresden, Germany
| | - Gunar Fabig
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Dresden, Dresden, Germany
| | - Michele Solimena
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany
- German Center for Diabetes Research, Neuherberg, Germany
- DFG Cluster of Excellence 'Physics of Life', TU Dresden, Dresden, Germany
| | - Martin Weigert
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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Murase S, Mantani Y, Ohno N, Shimada A, Nakanishi S, Morishita R, Yokoyama T, Hoshi N. Regional differences in the ultrastructure of mucosal macrophages in the rat large intestine. Cell Tissue Res 2024; 396:245-253. [PMID: 38485763 DOI: 10.1007/s00441-024-03883-w] [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: 09/06/2023] [Accepted: 02/25/2024] [Indexed: 04/28/2024]
Abstract
We previously clarified the histological characteristics of macrophages in the rat small intestine using serial block-face scanning electron microscopy (SBF-SEM). However, the regional differences in the characteristics of macrophages throughout the large intestine remain unknown. Here, we performed a pilot study to explore the regional differences in the ultrastructure of mucosal macrophages in the large intestine by using SBF-SEM analysis. SBF-SEM analysis conducted on the luminal side of the cecum and descending colon revealed macrophages as amorphous cells possessing abundant lysosomes and vacuoles. Macrophages in the cecum exhibited a higher abundance of lysosomes and a lower abundance of vacuoles than those in the descending colon. Macrophages with many intraepithelial cellular processes were observed beneath the intestinal superficial epithelium in the descending colon. Moreover, macrophages in contact with nerve fibers were more prevalent in the cecum than in the descending colon, and a subset of them surrounded a nerve bundle only in the cecum. In conclusion, the present pilot study suggested that the quantity of some organelles (lysosomes and vacuoles) in macrophages differed between the cecum and the descending colon and that there were some region-specific subsets of macrophages like nerve-associated macrophages in the cecum.
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Affiliation(s)
- Shota Murase
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-Cho, Nada-Ku, Kobe, Hyogo, 657-8501, Japan
| | - Youhei Mantani
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-Cho, Nada-Ku, Kobe, Hyogo, 657-8501, Japan.
| | - Nobuhiko Ohno
- Department of Anatomy, Division of Histology and Cell Biology, Jichi Medical University, School of Medicine, Shimotsuke, Tochigi, 329-0498, Japan
- Division of Ultrastructural Research, National Institute for Physiological Sciences, Okazaki, Aichi, 444-8787, Japan
| | - Asaka Shimada
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-Cho, Nada-Ku, Kobe, Hyogo, 657-8501, Japan
| | - Satoki Nakanishi
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-Cho, Nada-Ku, Kobe, Hyogo, 657-8501, Japan
| | - Rinako Morishita
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-Cho, Nada-Ku, Kobe, Hyogo, 657-8501, Japan
| | - Toshifumi Yokoyama
- Laboratory of Animal Molecular Morphology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-Cho, Nada-Ku, Kobe, Hyogo, 657-8501, Japan
| | - Nobuhiko Hoshi
- Laboratory of Animal Molecular Morphology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-Cho, Nada-Ku, Kobe, Hyogo, 657-8501, Japan
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Leclerc S, Gupta A, Ruokolainen V, Chen JH, Kunnas K, Ekman AA, Niskanen H, Belevich I, Vihinen H, Turkki P, Perez-Berna AJ, Kapishnikov S, Mäntylä E, Harkiolaki M, Dufour E, Hytönen V, Pereiro E, McEnroe T, Fahy K, Kaikkonen MU, Jokitalo E, Larabell CA, Weinhardt V, Mattola S, Aho V, Vihinen-Ranta M. Progression of herpesvirus infection remodels mitochondrial organization and metabolism. PLoS Pathog 2024; 20:e1011829. [PMID: 38620036 PMCID: PMC11045090 DOI: 10.1371/journal.ppat.1011829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 04/25/2024] [Accepted: 03/12/2024] [Indexed: 04/17/2024] Open
Abstract
Viruses target mitochondria to promote their replication, and infection-induced stress during the progression of infection leads to the regulation of antiviral defenses and mitochondrial metabolism which are opposed by counteracting viral factors. The precise structural and functional changes that underlie how mitochondria react to the infection remain largely unclear. Here we show extensive transcriptional remodeling of protein-encoding host genes involved in the respiratory chain, apoptosis, and structural organization of mitochondria as herpes simplex virus type 1 lytic infection proceeds from early to late stages of infection. High-resolution microscopy and interaction analyses unveiled infection-induced emergence of rough, thin, and elongated mitochondria relocalized to the perinuclear area, a significant increase in the number and clustering of endoplasmic reticulum-mitochondria contact sites, and thickening and shortening of mitochondrial cristae. Finally, metabolic analyses demonstrated that reactivation of ATP production is accompanied by increased mitochondrial Ca2+ content and proton leakage as the infection proceeds. Overall, the significant structural and functional changes in the mitochondria triggered by the viral invasion are tightly connected to the progression of the virus infection.
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Affiliation(s)
- Simon Leclerc
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Alka Gupta
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Visa Ruokolainen
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Jian-Hua Chen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Kari Kunnas
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Axel A. Ekman
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Henri Niskanen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ilya Belevich
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Finland
| | - Helena Vihinen
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Finland
| | - Paula Turkki
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ana J. Perez-Berna
- MISTRAL Beamline-Experiments Division, ALBA Synchrotron Light Source, Cerdanyola del Valles, Barcelona, Spain
| | | | - Elina Mäntylä
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Maria Harkiolaki
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK; Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, United Kingdom
| | - Eric Dufour
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Vesa Hytönen
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab laboratories, Tampere, Finland
| | - Eva Pereiro
- MISTRAL Beamline-Experiments Division, ALBA Synchrotron Light Source, Cerdanyola del Valles, Barcelona, Spain
| | | | | | - Minna U. Kaikkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Finland
| | - Carolyn A. Larabell
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Venera Weinhardt
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Salla Mattola
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Vesa Aho
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Maija Vihinen-Ranta
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
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Lachiondo-Ortega S, Rejano-Gordillo CM, Simon J, Lopitz-Otsoa F, C Delgado T, Mazan-Mamczarz K, Goikoetxea-Usandizaga N, Zapata-Pavas LE, García-Del Río A, Guerra P, Peña-Sanfélix P, Hermán-Sánchez N, Al-Abdulla R, Fernandez-Rodríguez C, Azkargorta M, Velázquez-Cruz A, Guyon J, Martín C, Zalamea JD, Egia-Mendikute L, Sanz-Parra A, Serrano-Maciá M, González-Recio I, Gonzalez-Lopez M, Martínez-Cruz LA, Pontisso P, Aransay AM, Barrio R, Sutherland JD, Abrescia NGA, Elortza F, Lujambio A, Banales JM, Luque RM, Gahete MD, Palazón A, Avila MA, G Marin JJ, De S, Daubon T, Díaz-Quintana A, Díaz-Moreno I, Gorospe M, Rodríguez MS, Martínez-Chantar ML. SUMOylation controls Hu antigen R posttranscriptional activity in liver cancer. Cell Rep 2024; 43:113924. [PMID: 38507413 PMCID: PMC11025316 DOI: 10.1016/j.celrep.2024.113924] [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: 09/30/2022] [Revised: 08/08/2023] [Accepted: 02/21/2024] [Indexed: 03/22/2024] Open
Abstract
The posttranslational modification of proteins critically influences many biological processes and is a key mechanism that regulates the function of the RNA-binding protein Hu antigen R (HuR), a hub in liver cancer. Here, we show that HuR is SUMOylated in the tumor sections of patients with hepatocellular carcinoma in contrast to the surrounding tissue, as well as in human cell line and mouse models of the disease. SUMOylation of HuR promotes major cancer hallmarks, namely proliferation and invasion, whereas the absence of HuR SUMOylation results in a senescent phenotype with dysfunctional mitochondria and endoplasmic reticulum. Mechanistically, SUMOylation induces a structural rearrangement of the RNA recognition motifs that modulates HuR binding affinity to its target RNAs, further modifying the transcriptomic profile toward hepatic tumor progression. Overall, SUMOylation constitutes a mechanism of HuR regulation that could be potentially exploited as a therapeutic strategy for liver cancer.
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Affiliation(s)
- Sofia Lachiondo-Ortega
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Claudia M Rejano-Gordillo
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Extremadura, University Institute of Biosanitary Research of Extremadura (INUBE), 06071 Badajoz, Spain; Biofisika Institute, Consejo Superior de Investigaciones Científicas (CSIC), Departamento Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Leioa, Spain
| | - Jorge Simon
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain
| | - Fernando Lopitz-Otsoa
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Teresa C Delgado
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Krystyna Mazan-Mamczarz
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA), Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Naroa Goikoetxea-Usandizaga
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - L Estefanía Zapata-Pavas
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Ana García-Del Río
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Pietro Guerra
- Unit of Internal Medicine and Hepatology (UIMH), Department of Medicine (DIMED), University of Padova, 35128 Padua, Italy
| | - Patricia Peña-Sanfélix
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Natalia Hermán-Sánchez
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), Department of Cell Biology, Physiology and Immunology of University of Córdoba, Reina Sofia University Hospital, CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), 14004 Córdoba, Spain
| | - Ruba Al-Abdulla
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universidad Miguel Hernández, Elche, Spain; Institute of Medical Biochemistry and Molecular Biology, University Medicine of Greifswald, 17475 Greifswald, Germany
| | - Carmen Fernandez-Rodríguez
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Mikel Azkargorta
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Proteomics Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Carlos III Networked Proteomics Platform (ProteoRed-ISCIII), 48160 Derio, Bizkaia, Spain
| | - Alejandro Velázquez-Cruz
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Joris Guyon
- University of Bordeaux, INSERM, BPH, U1219, 33000 Bordeaux, France; CHU de Bordeaux, Service de Pharmacologie Médicale, 33000 Bordeaux, France
| | - César Martín
- Biofisika Institute, Consejo Superior de Investigaciones Científicas (CSIC), Departamento Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Leioa, Spain
| | - Juan Diego Zalamea
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Leire Egia-Mendikute
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Arantza Sanz-Parra
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Marina Serrano-Maciá
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Irene González-Recio
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Monika Gonzalez-Lopez
- Genome Analysis Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Luis Alfonso Martínez-Cruz
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Patrizia Pontisso
- Unit of Internal Medicine and Hepatology (UIMH), Department of Medicine (DIMED), University of Padova, 35128 Padua, Italy
| | - Ana M Aransay
- Genome Analysis Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Rosa Barrio
- Ubiquitin-likes and Development Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - James D Sutherland
- Ubiquitin-likes and Development Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Nicola G A Abrescia
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Félix Elortza
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Proteomics Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Carlos III Networked Proteomics Platform (ProteoRed-ISCIII), 48160 Derio, Bizkaia, Spain
| | - Amaia Lujambio
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jesus M Banales
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain; Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain; Department of Biochemistry and Genetics, School of Sciences, University of Navarra, Pamplona, Spain
| | - Raúl M Luque
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), Department of Cell Biology, Physiology and Immunology of University of Córdoba, Reina Sofia University Hospital, CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), 14004 Córdoba, Spain
| | - Manuel D Gahete
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), Department of Cell Biology, Physiology and Immunology of University of Córdoba, Reina Sofia University Hospital, CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), 14004 Córdoba, Spain
| | - Asís Palazón
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Matias A Avila
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Hepatology Program, Centro de Investigación Médica Aplicada (CIMA), University of Navarra, Pamplona, Spain; Instituto de Investigaciones Sanitarias de Navarra (IdiSNA), Pamplona, Spain
| | - Jose J G Marin
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Experimental Hepatology and Drug Targeting (HEVEPHARM), Instituto de Investigación Biomédica de Salamanca (IBSAL), University of Salamanca, Salamanca, Spain
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA), Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Thomas Daubon
- University of Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux, France
| | - Antonio Díaz-Quintana
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA), Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Manuel S Rodríguez
- Laboratoire de Chimie de Coordination (LCC), UPR 8241, CNRS; IPBS-University of Toulouse III-Paul Sabatier, Toulouse, France
| | - María Luz Martínez-Chantar
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain.
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49
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Xu J, Liao C, Yin CC, Li G, Zhu Y, Sun F. In situ structural insights into the excitation-contraction coupling mechanism of skeletal muscle. SCIENCE ADVANCES 2024; 10:eadl1126. [PMID: 38507485 PMCID: PMC10954225 DOI: 10.1126/sciadv.adl1126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/12/2024] [Indexed: 03/22/2024]
Abstract
Excitation-contraction coupling (ECC) is a fundamental mechanism in control of skeletal muscle contraction and occurs at triad junctions, where dihydropyridine receptors (DHPRs) on transverse tubules sense excitation signals and then cause calcium release from the sarcoplasmic reticulum via coupling to type 1 ryanodine receptors (RyR1s), inducing the subsequent contraction of muscle filaments. However, the molecular mechanism remains unclear due to the lack of structural details. Here, we explored the architecture of triad junction by cryo-electron tomography, solved the in situ structure of RyR1 in complex with FKBP12 and calmodulin with the resolution of 16.7 Angstrom, and found the intact RyR1-DHPR supercomplex. RyR1s arrange into two rows on the terminal cisternae membrane by forming right-hand corner-to-corner contacts, and tetrads of DHPRs bind to RyR1s in an alternating manner, forming another two rows on the transverse tubule membrane. This unique arrangement is important for synergistic calcium release and provides direct evidence of physical coupling in ECC.
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Affiliation(s)
- Jiashu Xu
- Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenyi Liao
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chang-Cheng Yin
- Department of Biophysics, The Health Science Center, Peking University, Beijing 100191, China
- Electron Microscopy Analysis Laboratory, The Health Science Center, Peking University, Beijing 100191, China
- Center for Protein Science, Peking University, Beijing 100871, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yun Zhu
- Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fei Sun
- Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, 510005, China
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50
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Tomasch J, Kopejtka K, Bílý T, Gardiner AT, Gardian Z, Shivaramu S, Koblížek M, Kaftan D. A photoheterotrophic bacterium from Iceland has adapted its photosynthetic machinery to the long days of polar summer. mSystems 2024; 9:e0131123. [PMID: 38376261 PMCID: PMC10949492 DOI: 10.1128/msystems.01311-23] [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: 12/05/2023] [Accepted: 01/26/2024] [Indexed: 02/21/2024] Open
Abstract
During their long evolution, anoxygenic phototrophic bacteria have inhabited a wide variety of natural habitats and developed specific strategies to cope with the challenges of any particular environment. Expression, assembly, and safe operation of the photosynthetic apparatus must be regulated to prevent reactive oxygen species generation under illumination in the presence of oxygen. Here, we report on the photoheterotrophic Sediminicoccus sp. strain KRV36, which was isolated from a cold stream in north-western Iceland, 30 km south of the Arctic Circle. In contrast to most aerobic anoxygenic phototrophs, which stop pigment synthesis when illuminated, strain KRV36 maintained its bacteriochlorophyll synthesis even under continuous light. Its cells also contained between 100 and 180 chromatophores, each accommodating photosynthetic complexes that exhibit an unusually large carotenoid absorption spectrum. The expression of photosynthesis genes in dark-adapted cells was transiently downregulated in the first 2 hours exposed to light but recovered to the initial level within 24 hours. An excess of membrane-bound carotenoids as well as high, constitutive expression of oxidative stress response genes provided the required potential for scavenging reactive oxygen species, safeguarding bacteriochlorophyll synthesis and photosystem assembly. The unique cellular architecture and an unusual gene expression pattern represent a specific adaptation that allows the maintenance of anoxygenic phototrophy under arctic conditions characterized by long summer days with relatively low irradiance.IMPORTANCEThe photoheterotrophic bacterium Sediminicoccus sp. KRV36 was isolated from a cold stream in Iceland. It expresses its photosynthesis genes, synthesizes bacteriochlorophyll, and assembles functional photosynthetic complexes under continuous light in the presence of oxygen. Unraveling the molecular basis of this ability, which is exceptional among aerobic anoxygenic phototrophic species, will help to understand the evolution of bacterial photosynthesis in response to changing environmental conditions. It might also open new possibilities for genetic engineering of biotechnologically relevant phototrophs, with the aim of increasing photosynthetic activity and their tolerance to reactive oxygen species.
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Affiliation(s)
- Jürgen Tomasch
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Karel Kopejtka
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Tomáš Bílý
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Alastair T. Gardiner
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Zdenko Gardian
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Sahana Shivaramu
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - David Kaftan
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department Chemistry, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
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