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Jin J, van Gils SR, Zandieh-Doulabi B, Schoenmaker T, Klein-Nulend J, Nolte PA. Effect of endolysin XZ.700 on monocyte differentiation into osteoclasts and foreign body giant cells. Biochem Biophys Res Commun 2025; 764:151796. [PMID: 40253910 DOI: 10.1016/j.bbrc.2025.151796] [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: 02/08/2025] [Revised: 03/26/2025] [Accepted: 04/09/2025] [Indexed: 04/22/2025]
Abstract
Periprosthetic joint infections due to biofilm formation are a major concern in orthopaedic and dental implant surgery. Current treatment options use antibiotics, but antibiotic-resistant bacteria in the biofilm cause treatment failure. Bacteriophage-derived endolysin XZ.700 is highly promising to fight anti-microbial resistance, since it exhibits potent anti-biofilm activity and low cell toxicity. However, whether it affects immunomodulatory cell formation is currently unknown. Therefore, this study aimed to determine whether endolysin XZ.700 affects monocyte differentiation into osteoclasts and/or foreign body giant cells in vitro. Formation of multinucleated osteoclasts and foreign body giant cells from CD14+ monocytes cultured without/with endolysin XZ.700 (25, 50, 75 μg/ml) was assessed after 7, 14, and 21 days, as well as differentiation, multinucleation, and cell activation-related gene expression. Endolysin XZ.700 decreased formation of osteoclasts with 3-5 nuclei/cell, but increased those with >10 nuclei/cell after 21 days, resulting in overall inhibition of total osteoclast formation. The formation of foreign body giant cells with 3-5 nuclei/cell, but not 6-10 or >10 nuclei/cell, was significantly decreased by endolysin XZ.700 at all time points. Only 25 μg/ml endolysin XZ.700 decreased total foreign body giant cell formation after 21 days. Endolysin XZ.700 downregulated differentiation-related gene expression, but upregulated cytokine-related gene expression in monocytes differentiating into osteoclasts or foreign body giant cells. In conclusion, the biofilm-reducing agent endolysin XZ.700 decreases the formation of immunomodulatory cells, i.e. foreign body giant cells and osteoclasts, indicating that it might be highly promising as a novel antimicrobial, with short term administration as the safest mode of treatment.
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Affiliation(s)
- Jianfeng Jin
- Department of Oral Cell Biology, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Gustav Mahlerlaan 3004, 1081 LA, Amsterdam, the Netherlands.
| | - Sterre R van Gils
- Department of Oral Cell Biology, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Gustav Mahlerlaan 3004, 1081 LA, Amsterdam, the Netherlands.
| | - Behrouz Zandieh-Doulabi
- Department of Oral Cell Biology, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Gustav Mahlerlaan 3004, 1081 LA, Amsterdam, the Netherlands.
| | - Ton Schoenmaker
- Department of Periodontology, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Gustav Mahlerlaan 3004, 1081 LA, Amsterdam, the Netherlands.
| | - Jenneke Klein-Nulend
- Department of Oral Cell Biology, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Gustav Mahlerlaan 3004, 1081 LA, Amsterdam, the Netherlands.
| | - Peter A Nolte
- Department of Oral Cell Biology, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Gustav Mahlerlaan 3004, 1081 LA, Amsterdam, the Netherlands; Department of Orthopedic Surgery, Spaarne Gasthuis, Spaarnepoort 1, Hoofddorp, 2134 TM, the Netherlands.
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2
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Niu L, Swingler TE, Suelzu C, Ersek A, Orriss IR, Barter MJ, Hayman DJ, Young DA, Horwood N, Clark IM. The microRNA-455 null mouse shows dysregulated bone turnover. JBMR Plus 2025; 9:ziaf007. [PMID: 39963339 PMCID: PMC11831985 DOI: 10.1093/jbmrpl/ziaf007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Revised: 12/18/2024] [Accepted: 01/09/2025] [Indexed: 02/20/2025] Open
Abstract
A wide range of specific microRNAs have been shown to have either positive or negative effects on osteoblast differentiation and function, with consequent changes in postnatal bone mass. A number of specific targets have been identified. We previously used CrispR-Cas9 to make a miR-455 null mouse, characterizing a behavioral phenotype with age. The current study identifies a bone phenotype, starting in younger animals. At 3 weeks of age, the miR-455 null mice (both male and female) display increased length of both long bones and vertebrae and, while this difference diminishes across 1 year, it remains significant. Increased bone formation in vivo is mirrored by an increase in osteogenesis from bone marrow-derived stem cells in vitro. This is accompanied by a decrease in osteoclastogenesis and osteoclast function. MicroCT analyses show increased trabecular bone and less porosity/decreased separation in the miR-455 null mouse, suggesting a more dense and stronger bone at 3 weeks of age; these differences normalize by 1 year. Gain-of-function and loss-of-function datasets show that FGF18 expression is regulated by miR-455 and FGF18 was validated as a direct target of miR-455. The regulation of FGF18 by miR-455 is a likely mediator of its effect on bone.
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Affiliation(s)
- Lingzi Niu
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Tracey E Swingler
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Caterina Suelzu
- Norwich Medical School, University of East Anglia, Norwich, NR4 7UQ, United Kingdom
| | - Adel Ersek
- Norwich Medical School, University of East Anglia, Norwich, NR4 7UQ, United Kingdom
| | - Isabel R Orriss
- Comparative Biomedical Sciences, Royal Veterinary College, London, NW1 0TU, United Kingdom
| | - Matthew J Barter
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom
| | - Dan J Hayman
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom
| | - David A Young
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom
| | - Nicole Horwood
- Norwich Medical School, University of East Anglia, Norwich, NR4 7UQ, United Kingdom
| | - Ian M Clark
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
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3
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Manne SKR, Martin B, Roy T, Neilson R, Peters R, Chillara M, Lary CW, Motyl KJ, Wan M. NOISe: Nuclei-Aware Osteoclast Instance Segmentation for Mouse-to-Human Domain Transfer. CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION WORKSHOPS. IEEE COMPUTER SOCIETY CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION. WORKSHOPS 2024; 2024:6926-6935. [PMID: 39659628 PMCID: PMC11629985 DOI: 10.1109/cvprw63382.2024.00686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2024]
Abstract
Osteoclast cell image analysis plays a key role in osteoporosis research, but it typically involves extensive manual image processing and hand annotations by a trained expert. In the last few years, a handful of machine learning approaches for osteoclast image analysis have been developed, but none have addressed the full instance segmentation task required to produce the same output as that of the human expert led process. Furthermore, none of the prior, fully automated algorithms have publicly available code, pretrained models, or annotated datasets, inhibiting reproduction and extension of their work. We present a new dataset with ~2 × 105 expert annotated mouse osteoclast masks, together with a deep learning instance segmentation method which works for both in vitro mouse osteoclast cells on plastic tissue culture plates and human osteoclast cells on bone chips. To our knowledge, this is the first work to automate the full osteoclast instance segmentation task. Our method achieves a performance of 0.82 mAP0.5 (mean average precision at intersection-over-union threshold of 0.5) in cross validation for mouse osteoclasts. We present a novel nuclei-aware osteoclast instance segmentation training strategy (NOISe) based on the unique biology of osteoclasts, to improve the model's generalizability and boost the mAP0.5 from 0.60 to 0.82 on human osteoclasts. We publish our annotated mouse osteoclast image dataset, instance segmentation models, and code at github.com/michaelwwan/noise to enable reproducibility and to provide a public tool to accelerate osteoporosis research.
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Affiliation(s)
| | | | | | | | | | | | | | - Katherine J. Motyl
- MaineHealth Institute for Research
- University of Maine
- Tufts University School of Medicine
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4
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Davies BK, Hibbert AP, Roberts SJ, Roberts HC, Tickner JC, Holdsworth G, Arnett TR, Orriss IR. A Machine Learning-Based Image Segmentation Method to Quantify In Vitro Osteoclast Culture Endpoints. Calcif Tissue Int 2023; 113:437-448. [PMID: 37566229 PMCID: PMC10516805 DOI: 10.1007/s00223-023-01121-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/29/2023] [Indexed: 08/12/2023]
Abstract
Quantification of in vitro osteoclast cultures (e.g. cell number) often relies on manual counting methods. These approaches are labour intensive, time consuming and result in substantial inter- and intra-user variability. This study aimed to develop and validate an automated workflow to robustly quantify in vitro osteoclast cultures. Using ilastik, a machine learning-based image analysis software, images of tartrate resistant acid phosphatase-stained mouse osteoclasts cultured on dentine discs were used to train the ilastik-based algorithm. Assessment of algorithm training showed that osteoclast numbers strongly correlated between manual- and automatically quantified values (r = 0.87). Osteoclasts were consistently faithfully segmented by the model when visually compared to the original reflective light images. The ability of this method to detect changes in osteoclast number in response to different treatments was validated using zoledronate, ticagrelor, and co-culture with MCF7 breast cancer cells. Manual and automated counting methods detected a 70% reduction (p < 0.05) in osteoclast number, when cultured with 10 nM zoledronate and a dose-dependent decrease with 1-10 μM ticagrelor (p < 0.05). Co-culture with MCF7 cells increased osteoclast number by ≥ 50% irrespective of quantification method. Overall, an automated image segmentation and analysis workflow, which consistently and sensitively identified in vitro osteoclasts, was developed. Advantages of this workflow are (1) significantly reduction in user variability of endpoint measurements (93%) and analysis time (80%); (2) detection of osteoclasts cultured on different substrates from different species; and (3) easy to use and freely available to use along with tutorial resources.
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Affiliation(s)
- Bethan K Davies
- Department of Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, London, NW1 0TU, UK
- Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Andrew P Hibbert
- Department of Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, London, NW1 0TU, UK
| | - Scott J Roberts
- Department of Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, London, NW1 0TU, UK
| | - Helen C Roberts
- Department of Natural Sciences, Middlesex University, London, UK
| | - Jennifer C Tickner
- School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia
| | | | - Timothy R Arnett
- Department of Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, London, NW1 0TU, UK
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Isabel R Orriss
- Department of Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, London, NW1 0TU, UK.
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5
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Anwer DM, Gubinelli F, Kurt YA, Sarauskyte L, Jacobs F, Venuti C, Sandoval IM, Yang Y, Stancati J, Mazzocchi M, Brandi E, O’Keeffe G, Steece-Collier K, Li JY, Deierborg T, Manfredsson FP, Davidsson M, Heuer A. A comparison of machine learning approaches for the quantification of microglial cells in the brain of mice, rats and non-human primates. PLoS One 2023; 18:e0284480. [PMID: 37126506 PMCID: PMC10150977 DOI: 10.1371/journal.pone.0284480] [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: 12/13/2022] [Accepted: 03/31/2023] [Indexed: 05/02/2023] Open
Abstract
Microglial cells are brain-specific macrophages that swiftly react to disruptive events in the brain. Microglial activation leads to specific modifications, including proliferation, morphological changes, migration to the site of insult, and changes in gene expression profiles. A change in inflammatory status has been linked to many neurodegenerative diseases such as Parkinson's disease and Alzheimer's disease. For this reason, the investigation and quantification of microglial cells is essential for better understanding their role in disease progression as well as for evaluating the cytocompatibility of novel therapeutic approaches for such conditions. In the following study we implemented a machine learning-based approach for the fast and automatized quantification of microglial cells; this tool was compared with manual quantification (ground truth), and with alternative free-ware such as the threshold-based ImageJ and the machine learning-based Ilastik. We first trained the algorithms on brain tissue obtained from rats and non-human primate immunohistochemically labelled for microglia. Subsequently we validated the accuracy of the trained algorithms in a preclinical rodent model of Parkinson's disease and demonstrated the robustness of the algorithms on tissue obtained from mice, as well as from images provided by three collaborating laboratories. Our results indicate that machine learning algorithms can detect and quantify microglial cells in all the three mammalian species in a precise manner, equipotent to the one observed following manual counting. Using this tool, we were able to detect and quantify small changes between the hemispheres, suggesting the power and reliability of the algorithm. Such a tool will be very useful for investigation of microglial response in disease development, as well as in the investigation of compatible novel therapeutics targeting the brain. As all network weights and labelled training data are made available, together with our step-by-step user guide, we anticipate that many laboratories will implement machine learning-based quantification of microglial cells in their research.
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Affiliation(s)
- Danish M. Anwer
- Behavioural Neuroscience Laboratory, Department of Experimental Medical Sciences, Lund University Lund, Sweden
| | - Francesco Gubinelli
- Behavioural Neuroscience Laboratory, Department of Experimental Medical Sciences, Lund University Lund, Sweden
| | - Yunus A. Kurt
- Behavioural Neuroscience Laboratory, Department of Experimental Medical Sciences, Lund University Lund, Sweden
| | - Livija Sarauskyte
- Behavioural Neuroscience Laboratory, Department of Experimental Medical Sciences, Lund University Lund, Sweden
| | - Febe Jacobs
- Behavioural Neuroscience Laboratory, Department of Experimental Medical Sciences, Lund University Lund, Sweden
| | - Chiara Venuti
- Behavioural Neuroscience Laboratory, Department of Experimental Medical Sciences, Lund University Lund, Sweden
| | - Ivette M. Sandoval
- Barrow Neurological Institute, Parkinson’s Disease Research Unit, Department of Translational Neuroscience, Phoenix, Arizona, United States of America
| | - Yiyi Yang
- Experimental Neuroinflammation Laboratory, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Jennifer Stancati
- Translational Neuroscience, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States of America
| | - Martina Mazzocchi
- Brain Development and Repair Group, Department of Anatomy and Neuroscience University College Cork, Cork, Ireland
| | - Edoardo Brandi
- Neural Plasticity and Repair, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Gerard O’Keeffe
- Brain Development and Repair Group, Department of Anatomy and Neuroscience University College Cork, Cork, Ireland
| | - Kathy Steece-Collier
- Translational Neuroscience, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States of America
| | - Jia-Yi Li
- Neural Plasticity and Repair, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Tomas Deierborg
- Experimental Neuroinflammation Laboratory, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Fredric P. Manfredsson
- Barrow Neurological Institute, Parkinson’s Disease Research Unit, Department of Translational Neuroscience, Phoenix, Arizona, United States of America
| | - Marcus Davidsson
- Behavioural Neuroscience Laboratory, Department of Experimental Medical Sciences, Lund University Lund, Sweden
- Barrow Neurological Institute, Parkinson’s Disease Research Unit, Department of Translational Neuroscience, Phoenix, Arizona, United States of America
| | - Andreas Heuer
- Behavioural Neuroscience Laboratory, Department of Experimental Medical Sciences, Lund University Lund, Sweden
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6
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Brent MB, Emmanuel T. Contemporary Advances in Computer-Assisted Bone Histomorphometry and Identification of Bone Cells in Culture. Calcif Tissue Int 2023; 112:1-12. [PMID: 36309622 DOI: 10.1007/s00223-022-01035-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/13/2022] [Indexed: 01/07/2023]
Abstract
Static and dynamic bone histomorphometry and identification of bone cells in culture are labor-intensive and highly repetitive tasks. Several computer-assisted methods have been proposed to ease these tasks and to take advantage of the increased computational power available today. The present review aimed to provide an overview of contemporary methods utilizing specialized computer software to perform bone histomorphometry or identification of bone cells in culture. In addition, a brief historical perspective on bone histomorphometry is included. We identified ten publications using five different computer-assisted approaches (1) ImageJ and BoneJ; (2) Histomorph: OsteoidHisto, CalceinHisto, and TrapHisto; (3) Fiji/ImageJ2 and Trainable Weka Segmentation (TWS); (4) Visiopharm and artificial intelligence (AI); and (5) Osteoclast identification using deep learning with Single Shot Detection (SSD) architecture, Darknet and You Only Look Once (YOLO), or watershed algorithm (OC_Finder). The review also highlighted a substantial need for more validation studies that evaluate the accuracy of the new computational methods to the manual and conventional analyses of histological bone specimens and cells in culture using microscopy. However, a substantial evolution has occurred during the last decade to identify and separate bone cells and structures of interest. Most early studies have used simple image segmentation to separate structures of interest, whereas the most recent studies have utilized AI and deep learning. AI has been proposed to substantially decrease the amount of time needed for analyses and enable unbiased assessments. Despite the clear advantages of highly sophisticated computational methods, the limited nature of existing validation studies, particularly those that assess the accuracy of the third-generation methods compared to the second-generation methods, appears to be an important reason that these techniques have failed to gain wide acceptance.
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Affiliation(s)
- Mikkel Bo Brent
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, 8000, Aarhus, Denmark.
| | - Thomas Emmanuel
- Department of Dermatology, Aarhus University Hospital, 8200, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University Hospital, 8200, Aarhus, Denmark
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7
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Kohtala S, Nedal TMV, Kriesi C, Moen SH, Ma Q, Ødegaard KS, Standal T, Steinert M. Automated Quantification of Human Osteoclasts Using Object Detection. Front Cell Dev Biol 2022; 10:941542. [PMID: 35865628 PMCID: PMC9294346 DOI: 10.3389/fcell.2022.941542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/15/2022] [Indexed: 11/30/2022] Open
Abstract
A balanced skeletal remodeling process is paramount to staying healthy. The remodeling process can be studied by analyzing osteoclasts differentiated in vitro from mononuclear cells isolated from peripheral blood or from buffy coats. Osteoclasts are highly specialized, multinucleated cells that break down bone tissue. Identifying and correctly quantifying osteoclasts in culture are usually done by trained personnel using light microscopy, which is time-consuming and susceptible to operator biases. Using machine learning with 307 different well images from seven human PBMC donors containing a total of 94,974 marked osteoclasts, we present an efficient and reliable method to quantify human osteoclasts from microscopic images. An open-source, deep learning-based object detection framework called Darknet (YOLOv4) was used to train and test several models to analyze the applicability and generalizability of the proposed method. The trained model achieved a mean average precision of 85.26% with a correlation coefficient of 0.99 with human annotators on an independent test set and counted on average 2.1% more osteoclasts per culture than the humans. Additionally, the trained models agreed more than two independent human annotators, supporting a more reliable and less biased approach to quantifying osteoclasts while saving time and resources. We invite interested researchers to test their datasets on our models to further strengthen and validate the results.
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Affiliation(s)
- Sampsa Kohtala
- TrollLABS, Department of Mechanical and Industrial Engineering, Faculty of Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- *Correspondence: Sampsa Kohtala,
| | - Tonje Marie Vikene Nedal
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Carlo Kriesi
- TrollLABS, Department of Mechanical and Industrial Engineering, Faculty of Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Vitroscope AS, Trondheim, Norway
| | - Siv Helen Moen
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Qianli Ma
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Kristin Sirnes Ødegaard
- Department of Mechanical and Industrial Engineering, Faculty of Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Therese Standal
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Hematology, St. Olavs University Hospital, Trondheim, Norway
| | - Martin Steinert
- TrollLABS, Department of Mechanical and Industrial Engineering, Faculty of Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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8
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Wang X, Kittaka M, He Y, Zhang Y, Ueki Y, Kihara D. OC_Finder: Osteoclast Segmentation, Counting, and Classification Using Watershed and Deep Learning. FRONTIERS IN BIOINFORMATICS 2022; 2. [PMID: 35474753 PMCID: PMC9038109 DOI: 10.3389/fbinf.2022.819570] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Osteoclasts are multinucleated cells that exclusively resorb bone matrix proteins and minerals on the bone surface. They differentiate from monocyte/macrophage lineage cells in the presence of osteoclastogenic cytokines such as the receptor activator of nuclear factor-κB ligand (RANKL) and are stained positive for tartrate-resistant acid phosphatase (TRAP). In vitro osteoclast formation assays are commonly used to assess the capacity of osteoclast precursor cells for differentiating into osteoclasts wherein the number of TRAP-positive multinucleated cells is counted as osteoclasts. Osteoclasts are manually identified on cell culture dishes by human eyes, which is a labor-intensive process. Moreover, the manual procedure is not objective and results in lack of reproducibility. To accelerate the process and reduce the workload for counting the number of osteoclasts, we developed OC_Finder, a fully automated system for identifying osteoclasts in microscopic images. OC_Finder consists of cell image segmentation with a watershed algorithm and cell classification using deep learning. OC_Finder detected osteoclasts differentiated from wild-type and Sh3bp2KI/+ precursor cells at a 99.4% accuracy for segmentation and at a 98.1% accuracy for classification. The number of osteoclasts classified by OC_Finder was at the same accuracy level with manual counting by a human expert. OC_Finder also showed consistent performance on additional datasets collected with different microscopes with different settings by different operators. Together, successful development of OC_Finder suggests that deep learning is a useful tool to perform prompt and accurate unbiased classification and detection of specific cell types in microscopic images.
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Affiliation(s)
- Xiao Wang
- Department of Computer Science, Purdue University, West Lafayette, IN, United States
| | - Mizuho Kittaka
- Department of Biomedical Sciences and Comprehensive Care, Indiana University School of Dentistry, Indianapolis, IN, United States
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Yilin He
- School of Software Engineering, Shandong University, Jinan, China
| | - Yiwei Zhang
- Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Yasuyoshi Ueki
- Department of Biomedical Sciences and Comprehensive Care, Indiana University School of Dentistry, Indianapolis, IN, United States
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN, United States
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
- Purdue Cancer Research Institute, Purdue University, West Lafayette, IN, United States
- *Correspondence: Daisuke Kihara,
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9
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Sharma A, Clemens RA, Garcia O, Taylor DL, Wagner NL, Shepard KA, Gupta A, Malany S, Grodzinsky AJ, Kearns-Jonker M, Mair DB, Kim DH, Roberts MS, Loring JF, Hu J, Warren LE, Eenmaa S, Bozada J, Paljug E, Roth M, Taylor DP, Rodrigue G, Cantini P, Smith AW, Giulianotti MA, Wagner WR. Biomanufacturing in low Earth orbit for regenerative medicine. Stem Cell Reports 2021; 17:1-13. [PMID: 34971562 PMCID: PMC8758939 DOI: 10.1016/j.stemcr.2021.12.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 02/06/2023] Open
Abstract
Research in low Earth orbit (LEO) has become more accessible. The 2020 Biomanufacturing in Space Symposium reviewed space-based regenerative medicine research and discussed leveraging LEO to advance biomanufacturing for regenerative medicine applications. The symposium identified areas where financial investments could stimulate advancements overcoming technical barriers. Opportunities in disease modeling, stem-cell-derived products, and biofabrication were highlighted. The symposium will initiate a roadmap to a sustainable market for regenerative medicine biomanufacturing in space. This perspective summarizes the 2020 Biomanufacturing in Space Symposium, highlights key biomanufacturing opportunities in LEO, and lays the framework for a roadmap to regenerative medicine biomanufacturing in space.
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Affiliation(s)
- Arun Sharma
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | | | - Orquidea Garcia
- Johnson & Johnson 3D Printing Innovation & Customer Solutions, Johnson & Johnson Services, Inc., Irvine, CA, USA
| | - D Lansing Taylor
- University of Pittsburgh Drug Discovery Institute and Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Kelly A Shepard
- California Institute for Regenerative Medicine, Oakland, CA, USA
| | | | - Siobhan Malany
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Alan J Grodzinsky
- Departments of Biological Engineering, Mechanical Engineering and Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mary Kearns-Jonker
- Department of Pathology and Human Anatomy, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Devin B Mair
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Deok-Ho Kim
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael S Roberts
- Center for the Advancement of Science in Space, Inc, Melbourne, FL, USA
| | | | - Jianying Hu
- Center for Computational Health IBM Research, Yorktown Heights, New York, NY, USA
| | - Lara E Warren
- Center for the Advancement of Science in Space, Inc, Melbourne, FL, USA
| | - Sven Eenmaa
- Center for the Advancement of Science in Space, Inc, Melbourne, FL, USA
| | - Joe Bozada
- Joseph M. Katz Graduate School of Business, University of Pittsburgh, Pittsburgh, PA, USA
| | - Eric Paljug
- Joseph M. Katz Graduate School of Business, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Gary Rodrigue
- Center for the Advancement of Science in Space, Inc, Melbourne, FL, USA
| | - Patrick Cantini
- McGowan Institute for Regenerative Medicine, Pittsburgh, PA, USA
| | - Amelia W Smith
- Center for the Advancement of Science in Space, Inc, Melbourne, FL, USA
| | - Marc A Giulianotti
- Center for the Advancement of Science in Space, Inc, Melbourne, FL, USA.
| | - William R Wagner
- McGowan Institute for Regenerative Medicine, Pittsburgh, PA, USA; Departments of Surgery, Bioengineering, Chemical Engineering, University of Pittsburgh, Pittsburgh, PA, USA.
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