1
|
Ma H, Zhang T. Histone demethylase KDM3B mediates matrix stiffness-induced osteogenic differentiation of adipose-derived stem cells. Arch Biochem Biophys 2024; 757:110028. [PMID: 38768746 DOI: 10.1016/j.abb.2024.110028] [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: 09/29/2023] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
Biomechanical signals in the extracellular niche are considered promising for programming the lineage specification of stem cells. Recent studies have reported that biomechanics, such as the microstructure of nanomaterials, can induce adipose-derived stem cells (ASCs) to differentiate into osteoblasts, mediating gene regulation at the epigenetic level. Therefore, in this study, transcriptome expression levels of histone demethylases in ASCs were screened after treatment with different matrix stiffnesses, and histone lysine demethylase 3B (KDM3B) was found to promote osteogenic differentiation of ASCs in response to matrix stiffness, indicating a positive modulatory effect on this biological process. ASCs exhibited widespread and polygonal shapes with a distinct bundle-like expression of vinculin parallel to the axial cytoskeleton along the cell margins on the stiff matrix rather than round shapes with a smeared and shorter expression on the soft matrix. Comparatively rigid polydimethylsiloxane material directed ASCs into an osteogenic phenotype in inductive culture media via the upregulation of osteocalcin, alkaline phosphatase, and runt-related transcription factor 2. Treatment with KDM3B-siRNA decreased the expression of osteogenic differentiation markers and impaired mitochondrial dynamics and mitochondrial membrane potential. These results illustrate the critical role of KDM3B in the biomechanics-induced osteogenic commitment of ASCs and provide new avenues for the further application of stem cells as potential therapeutics for bone regeneration.
Collapse
Affiliation(s)
- Huangshui Ma
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China.
| | - Tao Zhang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China.
| |
Collapse
|
2
|
Zhang Y, Chen S, Huang C, Dai Y, Zhu S, Wang R, Gou X. Dynamic regulation of stem cell adhesion and differentiation on degradable piezoelectric poly (L-lactic acid) (PLLA) nanofibers. Biomed Eng Lett 2024; 14:775-784. [PMID: 38946806 PMCID: PMC11208363 DOI: 10.1007/s13534-024-00374-3] [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: 10/06/2023] [Revised: 01/25/2024] [Accepted: 03/19/2024] [Indexed: 07/02/2024] Open
Abstract
Degradable piezoelectric materials possess significant potential for application in the realm of bone tissue regeneration. However, the correlation between cell regulation mechanisms and the dynamic variation caused by material degradation has not been explained, hindering the optimization of material design and its in vivo application. Herein, piezoelectric poly (L-lactic acid) (PLLA) nanofibers with different molecular weights (MW) were fabricated, and the effects of their piezoelectric properties, structural morphology, and material products during degradation on the adhesion and osteogenic differentiation of mesenchymal stem cells (MSCs) were investigated. Our results demonstrated that cell adhesion-mediated piezoelectric stimulation could significantly enhance cell spreading, cell orientation, and upregulate the expression of calmodulin, which further triggers downstream signaling cascade to regulate osteogenic differentiation markers of type I collagen and runt-related transcription factor 2. Additionally, during the degradation of the nanofibers, the piezoelectric properties of PLLA weakened, the fibrous structure gradually diminished, and pH levels in the vicinity decreased, which resulting in reduced osteogenic differentiation capability of MSCs. However, nanofibers with higher MW (280 kDa) have the ability to maintain the fibrous morphology and piezoelectricity for a longer time, which can regulate the osteogenic differentiation of stem cells for more than 4 weeks. These findings have provide a new insight to correlate cell behavior with MW and the biodegradability of piezopolymers, which revealed an active method for cell regulation through material optimization for bone tissue engineering in near future.
Collapse
Affiliation(s)
- Yimeng Zhang
- Institute of Biomedical Engineering, College of Medicine, Southwest Jiaotong University, Chengdu, 610031 China
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education and Materials Science and Engineering, Southwest Jiaotong University, Chengdu, 610031 China
| | - Song Chen
- Department of Orthopaedics, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083 China
| | - Chenjun Huang
- Institute of Biomedical Engineering, College of Medicine, Southwest Jiaotong University, Chengdu, 610031 China
| | - Yujie Dai
- Institute of Biomedical Engineering, College of Medicine, Southwest Jiaotong University, Chengdu, 610031 China
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education and Materials Science and Engineering, Southwest Jiaotong University, Chengdu, 610031 China
| | - Shaomei Zhu
- Institute of Biomedical Engineering, College of Medicine, Southwest Jiaotong University, Chengdu, 610031 China
| | - Ran Wang
- BGI Research, Shenzhen, 518083 China
| | - Xue Gou
- Institute of Biomedical Engineering, College of Medicine, Southwest Jiaotong University, Chengdu, 610031 China
| |
Collapse
|
3
|
Greatbatch CJ, Lu Q, Hung S, Tran SN, Wing K, Liang H, Han X, Zhou T, Siggs OM, Mackey DA, Liu GS, Cook AL, Powell JE, Craig JE, MacGregor S, Hewitt AW. Deep Learning-Based Identification of Intraocular Pressure-Associated Genes Influencing Trabecular Meshwork Cell Morphology. OPHTHALMOLOGY SCIENCE 2024; 4:100504. [PMID: 38682030 PMCID: PMC11046128 DOI: 10.1016/j.xops.2024.100504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 05/01/2024]
Abstract
Purpose Genome-wide association studies have recently uncovered many loci associated with variation in intraocular pressure (IOP). Artificial intelligence (AI) can be used to interrogate the effect of specific genetic knockouts on the morphology of trabecular meshwork cells (TMCs) and thus, IOP regulation. Design Experimental study. Subjects Primary TMCs collected from human donors. Methods Sixty-two genes at 55 loci associated with IOP variation were knocked out in primary TMC lines. All cells underwent high-throughput microscopy imaging after being stained with a 5-channel fluorescent cell staining protocol. A convolutional neural network was trained to distinguish between gene knockout and normal control cell images. The area under the receiver operator curve (AUC) metric was used to quantify morphological variation in gene knockouts to identify potential pathological perturbations. Main Outcome Measures Degree of morphological variation as measured by deep learning algorithm accuracy of differentiation from normal controls. Results Cells where LTBP2 or BCAS3 had been perturbed demonstrated the greatest morphological variation from normal TMCs (AUC 0.851, standard deviation [SD] 0.030; and AUC 0.845, SD 0.020, respectively). Of 7 multigene loci, 5 had statistically significant differences in AUC (P < 0.05) between genes, allowing for pathological gene prioritization. The mitochondrial channel most frequently showed the greatest degree of morphological variation (33.9% of cell lines). Conclusions We demonstrate a robust method for functionally interrogating genome-wide association signals using high-throughput microscopy and AI. Genetic variations inducing marked morphological variation can be readily identified, allowing for the gene-based dissection of loci associated with complex traits. Financial Disclosures Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
Collapse
Affiliation(s)
- Connor J. Greatbatch
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Qinyi Lu
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Sandy Hung
- Centre for Eye Research Australia, University of Melbourne, Melbourne, Victoria, Australia
| | - Son N. Tran
- Department of Information and Communication Technology, University of Tasmania, Hobart, Tasmania, Australia
| | - Kristof Wing
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Helena Liang
- Centre for Eye Research Australia, University of Melbourne, Melbourne, Victoria, Australia
| | - Xikun Han
- Statistical Genetics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Tiger Zhou
- Department of Ophthalmology, Flinders Medical Centre, Flinders University, Bedford Park, Australia
| | - Owen M. Siggs
- Cellular Genomics Group, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, School of Clinical Medicine, UNSW, Sydney, New South Wales, Australia
| | - David A. Mackey
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
- Lions Eye Institute, Centre for Ophthalmology and Visual Science, University of Western Australia, Perth, Western Australia, Australia
| | - Guei-Sheung Liu
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
- Centre for Eye Research Australia, University of Melbourne, Melbourne, Victoria, Australia
| | - Anthony L. Cook
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, Tasmania, Australia
| | - Joseph E. Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- UNSW Cellular Genomics Futures Institute, UNSW, Sydney, New South Wales, Australia
| | - Jamie E. Craig
- Department of Ophthalmology, Flinders Medical Centre, Flinders University, Bedford Park, Australia
| | - Stuart MacGregor
- Statistical Genetics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Alex W. Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
- Centre for Eye Research Australia, University of Melbourne, Melbourne, Victoria, Australia
| |
Collapse
|
4
|
Pan H, Wei Y, Zeng C, Yang G, Dong C, Wan W, Chen S. Hierarchically Assembled Nanofiber Scaffold Guides Long Bone Regeneration by Promoting Osteogenic/Chondrogenic Differentiation of Endogenous Mesenchymal Stem Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2309868. [PMID: 38259052 DOI: 10.1002/smll.202309868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/28/2023] [Indexed: 01/24/2024]
Abstract
Critical-sized segmental long bone defects represent a challenging clinical dilemma in the management of battlefield and trauma-related injuries. The residual bone marrow cavity of damaged long bones contains many bone marrow mesenchymal stem cells (BMSCs), which provide a substantial source of cells for bone repair. Thus, a three-dimensional (3D) vertically aligned nanofiber scaffold (VAS) is developed with long channels and large pore size. The pore of VAS toward the bone marrow cavity after transplantation, enables the scaffolds to recruit BMSCs from the bone marrow cavity to the defect area. In vivo, it is found that VAS can significantly shorten gap distance and promote new bone formation compared to the control and collagen groups after 4 and 8 weeks of implantation. The single-cell sequencing results discovered that the 3D nanotopography of VAS can promote BMSCs differentiation to chondrocytes and osteoblasts, and up-regulate related gene expression, resulting in enhancing the activities of bone regeneration, endochondral ossification, bone trabecula formation, bone mineralization, maturation, and remodeling. The Alcian blue and bone morphogenetic protein 2 (BMP-2) immunohistochemical staining verified significant cartilage formation and bone formation in the VAS group, corresponding to the single-cell sequencing results. The study can inspire the design of next-generation scaffolds for effective long-bone regeneration is expected by the authors.
Collapse
Affiliation(s)
- Hao Pan
- Department of Orthopaedic Surgery, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325015, China
- Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Yuxuan Wei
- Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
- Department of Foot and Ankle Surgery, Center for Orthopaedic Surgery, the Third Affiliated Hospital of Southern Medical University. Guangzhou, Guangdong, 510630, China
| | - Canjun Zeng
- Department of Foot and Ankle Surgery, Center for Orthopaedic Surgery, the Third Affiliated Hospital of Southern Medical University. Guangzhou, Guangdong, 510630, China
| | - Ganghua Yang
- Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
- Department of Orthopaedic Surgery, the Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Chao Dong
- Department of Orthopedics, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Wenbing Wan
- Department of Orthopaedic Surgery, the Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Shixuan Chen
- Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
- Department of Wound Healing, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
| |
Collapse
|
5
|
Di Buduo CA, Lunghi M, Kuzmenko V, Laurent P, Della Rosa G, Del Fante C, Dalle Nogare DE, Jug F, Perotti C, Eto K, Pecci A, Redwan IN, Balduini A. Bioprinting Soft 3D Models of Hematopoiesis using Natural Silk Fibroin-Based Bioink Efficiently Supports Platelet Differentiation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308276. [PMID: 38514919 PMCID: PMC11095152 DOI: 10.1002/advs.202308276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/09/2024] [Indexed: 03/23/2024]
Abstract
Hematopoietic stem and progenitor cells (HSPCs) continuously generate platelets throughout one's life. Inherited Platelet Disorders affect ≈ 3 million individuals worldwide and are characterized by defects in platelet formation or function. A critical challenge in the identification of these diseases lies in the absence of models that facilitate the study of hematopoiesis ex vivo. Here, a silk fibroin-based bioink is developed and designed for 3D bioprinting. This bioink replicates a soft and biomimetic environment, enabling the controlled differentiation of HSPCs into platelets. The formulation consisting of silk fibroin, gelatin, and alginate is fine-tuned to obtain a viscoelastic, shear-thinning, thixotropic bioink with the remarkable ability to rapidly recover after bioprinting and provide structural integrity and mechanical stability over long-term culture. Optical transparency allowed for high-resolution imaging of platelet generation, while the incorporation of enzymatic sensors allowed quantitative analysis of glycolytic metabolism during differentiation that is represented through measurable color changes. Bioprinting patient samples revealed a decrease in metabolic activity and platelet production in Inherited Platelet Disorders. These discoveries are instrumental in establishing reference ranges for classification and automating the assessment of treatment responses. This model has far-reaching implications for application in the research of blood-related diseases, prioritizing drug development strategies, and tailoring personalized therapies.
Collapse
Affiliation(s)
| | - Marco Lunghi
- Department of Molecular MedicineUniversity of PaviaPavia27100Italy
| | | | | | | | - Claudia Del Fante
- Immunohaematology and Transfusion ServiceI.R.C.C.S. Policlinico S. Matteo FoundationPavia27100Italy
| | | | | | - Cesare Perotti
- Immunohaematology and Transfusion ServiceI.R.C.C.S. Policlinico S. Matteo FoundationPavia27100Italy
| | - Koji Eto
- Department of Clinical ApplicationCenter for iPS Cell Research and Application (CiRA)Kyoto UniversityKyoto606‐8507Japan
- Department of Regenerative MedicineGraduate School of MedicineChiba UniversityChiba260‐8670Japan
| | - Alessandro Pecci
- Department of Internal MedicineI.R.C.C.S. Policlinico S. Matteo Foundation and University of PaviaPavia27100Italy
| | | | - Alessandra Balduini
- Department of Molecular MedicineUniversity of PaviaPavia27100Italy
- Department of Biomedical EngineeringTufts UniversityMedfordMA02155USA
| |
Collapse
|
6
|
Budhkar A, Tang Z, Liu X, Zhang X, Su J, Song Q. xSiGra: Explainable model for single-cell spatial data elucidation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.27.591458. [PMID: 38746321 PMCID: PMC11092461 DOI: 10.1101/2024.04.27.591458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Recent advancements in spatial imaging technologies have revolutionized the acquisition of high-resolution multi-channel images, gene expressions, and spatial locations at the single-cell level. Our study introduces xSiGra, an interpretable graph-based AI model, designed to elucidate interpretable features of identified spatial cell types, by harnessing multi-modal features from spatial imaging technologies. By constructing a spatial cellular graph with immunohistology images and gene expression as node attributes, xSiGra employs hybrid graph transformer models to delineate spatial cell types. Additionally, xSiGra integrates a novel variant of Grad-CAM component to uncover interpretable features, including pivotal genes and cells for various cell types, thereby facilitating deeper biological insights from spatial data. Through rigorous benchmarking against existing methods, xSiGra demonstrates superior performance across diverse spatial imaging datasets. Application of xSiGra on a lung tumor slice unveils the importance score of cells, illustrating that cellular activity is not solely determined by itself but also impacted by neighboring cells. Moreover, leveraging the identified interpretable genes, xSiGra reveals endothelial cell subset interacting with tumor cells, indicating its heterogeneous underlying mechanisms within the complex cellular communications.
Collapse
|
7
|
Arevalo J, Su E, van Dijk R, Carpenter AE, Singh S. Evaluating batch correction methods for image-based cell profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.15.558001. [PMID: 37745478 PMCID: PMC10516049 DOI: 10.1101/2023.09.15.558001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
High-throughput image-based profiling platforms are powerful technologies capable of collecting data from billions of cells exposed to thousands of perturbations in a time- and cost-effective manner. Therefore, image-based profiling data has been increasingly used for diverse biological applications, such as predicting drug mechanism of action or gene function. However, batch effects pose severe limitations to community-wide efforts to integrate and interpret image-based profiling data collected across different laboratories and equipment. To address this problem, we benchmarked seven high-performing scRNA-seq batch correction techniques, representing diverse approaches, using a newly released Cell Painting dataset, the largest publicly accessible image-based dataset. We focused on five different scenarios with varying complexity, and we found that Harmony, a mixture-model based method, consistently outperformed the other tested methods. Our proposed framework, benchmark, and metrics can additionally be used to assess new batch correction methods in the future. Overall, this work paves the way for improvements that allow the community to make best use of public Cell Painting data for scientific discovery.
Collapse
Affiliation(s)
- John Arevalo
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ellen Su
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Robert van Dijk
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Anne E Carpenter
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Shantanu Singh
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| |
Collapse
|
8
|
Mustafayev F, Youn J, Hanif A, Kim DS. A Perforated Plate-Based Cell Showering Device for Uniform Cell Distribution over Various Culture Substrates. ACS Biomater Sci Eng 2024; 10:620-627. [PMID: 38048415 DOI: 10.1021/acsbiomaterials.3c01203] [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: 12/06/2023]
Abstract
Cell distribution is one of the primary factors that can affect cell morphology and behaviors, as it determines cell-cell interactions. Despite the importance of cell distribution, the seeding process of in vitro cell culture still highly relies on the traditional method using manual pipetting. Because manual pipetting cannot ensure a uniform cell distribution and has the possibility of compromising experimental reproducibility, an accurate and systemic seeding method that enables uniform cell seeding over versatile culture substrates is required. Here, we developed a perforated plate-based cell seeding device called the CellShower, which enabled uniform cell seeding over a large area of cell culture substrates. The working principles of the CellShower are based on the laminar filling flow and capillary force in microfluidics, and the design of the CellShower was optimized with numerical simulations. The versatility of the CellShower in view of uniform cell seeding was demonstrated by applying it to various types of culture substrates from a conventional culture dish to culture substrates having nanotopography, porous structures, and 3D concave structures. The CellShower and its operating principles are expected to contribute to enhancing the accuracy and reproducibility of biological experiments.
Collapse
Affiliation(s)
- Farid Mustafayev
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37763, Republic of Korea
| | - Jaeseung Youn
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37763, Republic of Korea
| | - Adeela Hanif
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37763, Republic of Korea
| | - Dong Sung Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37763, Republic of Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH) Pohang, 37673, Republic of Korea
- Institute for Convergence Research and Education in Advanced Technology, Yonsei University, Seoul 03722, Republic of Korea
| |
Collapse
|
9
|
Choi JS, Doo HM, Kim B, Lee SH, Sung SK, Go G, Suarez A, Kim Y, Weon BM, Choi BO, Kim HJ, Kim DH. NanoIEA: A Nanopatterned Interdigitated Electrode Array-Based Impedance Assay for Real-Time Measurement of Aligned Endothelial Cell Barrier Functions. Adv Healthc Mater 2024; 13:e2301124. [PMID: 37820720 PMCID: PMC10841753 DOI: 10.1002/adhm.202301124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/18/2023] [Indexed: 10/13/2023]
Abstract
A nanopatterned interdigitated electrode array (nanoIEA)-based impedance assay is developed for quantitative real-time measurement of aligned endothelial cell (EC) barrier functions in vitro. A bioinspired poly(3,4-dihydroxy-L-phenylalanine) (poly (l-DOPA)) coating is applied to improve the human brain EC adhesion onto the Nafion nanopatterned surfaces. It is found that a poly (l-DOPA)-coated Nafion grooved nanopattern makes the human brain ECs orient along the nanopattern direction. Aligned human brain ECs on Nafion nanopatterns exhibit increased expression of genes encoding tight and adherens junction proteins. Aligned human brain ECs also have enhanced impedance and resistance versus unaligned ones. Treatment with a glycogen synthase kinase-3 inhibitor (GSK3i) further increases impedance and resistance, suggesting synergistic effects occur on the cell-cell tightness of in vitro human brain ECs via a combination of anisotropic matrix nanotopography and GSK3i treatment. It is found that this enhanced cell-cell tightness of the combined approach is accompanied by increased expression of claudin protein. These data demonstrate that the proposed nanoIEA assay integrated with poly (l-DOPA)-coated Nafion nanopatterns and interdigitated electrode arrays can make not only biomimetic aligned ECs, but also enable real-time measurement of the enhanced barrier functions of aligned ECs via tighter cell-cell junctions.
Collapse
Affiliation(s)
- Jong Seob Choi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, United States; Division of Advanced Materials Engineering, Kongju National University, Cheonan, Chungnam, 31080, South Korea
| | - Hyun Myung Doo
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, 06351, South Korea
| | - Byunggik Kim
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States
| | - Su Han Lee
- Digital Health Care Research Center, Gumi Electronics, and Information Technology Research Institute (GERI), Gumi, Gyeongbuk, 39253, South Korea
| | - Sang-keun Sung
- Digital Health Care Research Center, Gumi Electronics, and Information Technology Research Institute (GERI), Gumi, Gyeongbuk, 39253, South Korea
| | - Gwangjun Go
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, United States
| | - Allister Suarez
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, United States
| | - Yeseul Kim
- Soft Matter Physics Laboratory, School of Advanced Materials Science and Engineering, SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, South Korea
| | - Byung Mook Weon
- Soft Matter Physics Laboratory, School of Advanced Materials Science and Engineering, SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, South Korea
| | - Byung-Ok Choi
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, 06351, South Korea; Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Hyung Jin Kim
- School of Electrical & Electronic Engineering, Ulsan College, Ulsan, 44610, South Korea
| | - Deok-Ho Kim
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, United States
| |
Collapse
|
10
|
Xiao X, Kong Y, Li R, Wang Z, Lu H. Transformer with convolution and graph-node co-embedding: An accurate and interpretable vision backbone for predicting gene expressions from local histopathological image. Med Image Anal 2024; 91:103040. [PMID: 38007979 DOI: 10.1016/j.media.2023.103040] [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: 03/27/2023] [Revised: 11/04/2023] [Accepted: 11/17/2023] [Indexed: 11/28/2023]
Abstract
Inferring gene expressions from histopathological images has long been a fascinating yet challenging task, primarily due to the substantial disparities between the two modality. Existing strategies using local or global features of histological images are suffering model complexity, GPU consumption, low interpretability, insufficient encoding of local features, and over-smooth prediction of gene expressions among neighboring sites. In this paper, we develop TCGN (Transformer with Convolution and Graph-Node co-embedding method) for gene expression estimation from H&E-stained pathological slide images. TCGN comprises a combination of convolutional layers, transformer encoders, and graph neural networks, and is the first to integrate these blocks in a general and interpretable computer vision backbone. Notably, TCGN uniquely operates with just a single spot image as input for histopathological image analysis, simplifying the process while maintaining interpretability. We validate TCGN on three publicly available spatial transcriptomic datasets. TCGN consistently exhibited the best performance (with median PCC 0.232). TCGN offers superior accuracy while keeping parameters to a minimum (just 86.241 million), and it consumes minimal memory, allowing it to run smoothly even on personal computers. Moreover, TCGN can be extended to handle bulk RNA-seq data while providing the interpretability. Enhancing the accuracy of omics information prediction from pathological images not only establishes a connection between genotype and phenotype, enabling the prediction of costly-to-measure biomarkers from affordable histopathological images, but also lays the groundwork for future multi-modal data modeling. Our results confirm that TCGN is a powerful tool for inferring gene expressions from histopathological images in precision health applications.
Collapse
Affiliation(s)
- Xiao Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; SJTU-Yale Joint Center for Biostatistics and Data Science, National Center for Translational Medicine, MoE Key Lab of Artificial Intelligence, AI Institute, Shanghai Jiao Tong University, Shanghai, China; Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, United States
| | - Yan Kong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; SJTU-Yale Joint Center for Biostatistics and Data Science, National Center for Translational Medicine, MoE Key Lab of Artificial Intelligence, AI Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Ronghan Li
- SJTU-Yale Joint Center for Biostatistics and Data Science, National Center for Translational Medicine, MoE Key Lab of Artificial Intelligence, AI Institute, Shanghai Jiao Tong University, Shanghai, China; Zhiyuan College, Shanghai Jiao Tong University, Shanghai, China
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, United States
| | - Hui Lu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; SJTU-Yale Joint Center for Biostatistics and Data Science, National Center for Translational Medicine, MoE Key Lab of Artificial Intelligence, AI Institute, Shanghai Jiao Tong University, Shanghai, China; NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Shanghai, China.
| |
Collapse
|
11
|
Song S, Mohsin E, Zhang R, Kuznetsov A, Shen L, Grossman RL, Weber CR, Khan AA. ATAT: Automated Tissue Alignment and Traversal in Spatial Transcriptomics with Self-Supervised Learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570839. [PMID: 38106010 PMCID: PMC10723486 DOI: 10.1101/2023.12.08.570839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Spatial transcriptomics (ST) has enhanced RNA analysis in tissue biopsies, but interpreting these data is challenging without expert input. We present Automated Tissue Alignment and Traversal (ATAT), a novel computational framework designed to enhance ST analysis in the context of multiple and complex tissue architectures and morphologies, such as those found in biopsies of the gastrointestinal tract. ATAT utilizes self-supervised contrastive learning on hematoxylin and eosin (H&E) stained images to automate the alignment and traversal of ST data. This approach addresses a critical gap in current ST analysis methodologies, which rely heavily on manual annotation and pathologist expertise to delineate regions of interest for accurate gene expression modeling. Our framework not only streamlines the alignment of multiple ST samples, but also demonstrates robustness in modeling gene expression transitions across specific regions. Additionally, we highlight the ability of ATAT to traverse complex tissue topologies in real-world cases from various individuals and conditions. Our method successfully elucidates differences in immune infiltration patterns across the intestinal wall, enabling the modeling of transcriptional changes across histological layers. We show that ATAT achieves comparable performance to the state-of-the-art method, while alleviating the burden of manual annotation and enabling alignment of tissue samples with complex morphologies.
Collapse
Affiliation(s)
- Steven Song
- Department of Computer Science, University of Chicago, IL 60637, USA
- Interdisciplinary Scientist Training Program, University of Chicago, Chicago, IL 60637, USA
| | - Emaan Mohsin
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Renyu Zhang
- Department of Computer Science, University of Chicago, IL 60637, USA
| | - Andrey Kuznetsov
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Le Shen
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Robert L. Grossman
- Department of Computer Science, University of Chicago, IL 60637, USA
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | | | - Aly A. Khan
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
- Institute for Population and Precision Health, University of Chicago, Chicago, IL 60637, USA
- Department of Family Medicine, University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
12
|
Pham D, Tan X, Balderson B, Xu J, Grice LF, Yoon S, Willis EF, Tran M, Lam PY, Raghubar A, Kalita-de Croft P, Lakhani S, Vukovic J, Ruitenberg MJ, Nguyen QH. Robust mapping of spatiotemporal trajectories and cell-cell interactions in healthy and diseased tissues. Nat Commun 2023; 14:7739. [PMID: 38007580 PMCID: PMC10676408 DOI: 10.1038/s41467-023-43120-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/01/2023] [Indexed: 11/27/2023] Open
Abstract
Spatial transcriptomics (ST) technologies generate multiple data types from biological samples, namely gene expression, physical distance between data points, and/or tissue morphology. Here we developed three computational-statistical algorithms that integrate all three data types to advance understanding of cellular processes. First, we present a spatial graph-based method, pseudo-time-space (PSTS), to model and uncover relationships between transcriptional states of cells across tissues undergoing dynamic change (e.g. neurodevelopment, brain injury and/or microglia activation, and cancer progression). We further developed a spatially-constrained two-level permutation (SCTP) test to study cell-cell interaction, finding highly interactive tissue regions across thousands of ligand-receptor pairs with markedly reduced false discovery rates. Finally, we present a spatial graph-based imputation method with neural network (stSME), to correct for technical noise/dropout and increase ST data coverage. Together, the algorithms that we developed, implemented in the comprehensive and fast stLearn software, allow for robust interrogation of biological processes within healthy and diseased tissues.
Collapse
Affiliation(s)
- Duy Pham
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Xiao Tan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Brad Balderson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Jun Xu
- Genome Innovation Hub, The University of Queensland, Brisbane, Australia
| | - Laura F Grice
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Sohye Yoon
- Genome Innovation Hub, The University of Queensland, Brisbane, Australia
| | - Emily F Willis
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Minh Tran
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Pui Yeng Lam
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Arti Raghubar
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | | | - Sunil Lakhani
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia
| | - Jana Vukovic
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Marc J Ruitenberg
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, Australia.
| | - Quan H Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.
- QIMR Berghofer Medical Research Institute, Herston, Australia.
| |
Collapse
|
13
|
Kholodenko BN, Kolch W, Rukhlenko OS. Reversing pathological cell states: the road less travelled can extend the therapeutic horizon. Trends Cell Biol 2023; 33:913-923. [PMID: 37263821 PMCID: PMC10593090 DOI: 10.1016/j.tcb.2023.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/15/2023] [Accepted: 04/17/2023] [Indexed: 06/03/2023]
Abstract
Acquisition of omics data advances at a formidable pace. Yet, our ability to utilize these data to control cell phenotypes and design interventions that reverse pathological states lags behind. Here, we posit that cell states are determined by core networks that control cell-wide networks. To steer cell fate decisions, core networks connecting genotype to phenotype must be reconstructed and understood. A recent method, cell state transition assessment and regulation (cSTAR), applies perturbation biology to quantify causal connections and mechanistically models how core networks influence cell phenotypes. cSTAR models are akin to digital cell twins enabling us to purposefully convert pathological states back to physiologically normal states. While this capability has a range of applications, here we discuss reverting oncogenic transformation.
Collapse
Affiliation(s)
- Boris N Kholodenko
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland; Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
| | - Oleksii S Rukhlenko
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| |
Collapse
|
14
|
Fang K, Müller S, Ueda M, Nakagawa Y, S Furukawa K, Ushida T, Ikoma T, Ito Y. Cyclic stretch modulates the cell morphology transition under geometrical confinement by covalently immobilized gelatin. J Mater Chem B 2023; 11:9155-9162. [PMID: 37455606 DOI: 10.1039/d3tb00421j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Fibroblasts geometrically confined by photo-immobilized gelatin micropatterns were subjected to cyclic stretch on the silicone elastomer. By using covalently micropatterned surfaces, the cell morphologies such as cell area and length were quantitatively investigated under a cyclic stretch for 20 hours. The mechanical forces did not affect the cell growth but significantly altered the cellular morphology on both non-patterned and micropatterned surfaces. It was found that cells on non-patterns showed increasing cell length and decreasing cell area under the stretch. The width of the strip micropatterns provided a different extent of contact guidance for fibroblasts. The highly extended cells on the 10 μm pattern under static conditions would perform a contraction behavior once treated by cyclic stretch. In contrast, cells with a low extension on the 2 μm pattern kept elongating according to the micropattern under the cyclic stretch. The vertical stretch induced an increase in cell area and length more than the parallel stretch in both the 10 μm and 2 μm patterns. These results provided new insights into cell behaviors under geometrical confinement in a dynamic biomechanical environment and may guide biomaterial design for tissue engineering in the future.
Collapse
Affiliation(s)
- Kun Fang
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
- Graduate School of Material Science and Engineering, Tokyo Institute of Technology, Meguro, 2-12-1 Ookayama, Tokyo 152-8550, Japan
| | - Stefan Müller
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Motoki Ueda
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yasuhiro Nakagawa
- Graduate School of Material Science and Engineering, Tokyo Institute of Technology, Meguro, 2-12-1 Ookayama, Tokyo 152-8550, Japan
| | - Katsuko S Furukawa
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-8656, Japan
| | - Takashi Ushida
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-8656, Japan
| | - Toshiyuki Ikoma
- Graduate School of Material Science and Engineering, Tokyo Institute of Technology, Meguro, 2-12-1 Ookayama, Tokyo 152-8550, Japan
| | - Yoshihiro Ito
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
- Graduate School of Material Science and Engineering, Tokyo Institute of Technology, Meguro, 2-12-1 Ookayama, Tokyo 152-8550, Japan
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| |
Collapse
|
15
|
Feng Y, Li M. Micropipette-assisted atomic force microscopy for single-cell 3D manipulations and nanomechanical measurements. NANOSCALE 2023; 15:13346-13358. [PMID: 37526589 DOI: 10.1039/d3nr02404k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Mechanical cues play a crucial role in regulating physiological and pathological processes, and atomic force microscopy (AFM) has become an important and standard tool for measuring the mechanical properties of single cells. In particular, providing a capability to manipulate cells in a three-dimensional (3D) space benefits enhancing the applications of AFM measurements in cell biology. Here, we present the complementary integration of AFM and micropipette micromanipulation, which allows precise 3D manipulations and nanomechanical measurements of single living cells. A micropipette micromanipulation system under the guidance of optical microscopy was established to isolate single living cells, and polydimethylsiloxane (PDMS) micropillar substrates were used to physically immobilize the isolated living cells for downstream AFM detection. The viscoelastic properties (Young's modulus, relaxation time, viscosity) of cells were quantitatively measured by AFM-based indentation assay. The effectiveness of micropipette-assisted AFM in single-cell analysis was confirmed on both living animal suspended cells and living animal adherent cells, showing dramatic changes in cell mechanics in different states and revealing the dynamics of single cells grown on micropillar arrays. The study demonstrates the great potential of a micropipette to aid AFM in single-cell manipulations for better accessing the mechanical cues involved in cellular processes, which will allow additional studies of single-cell mechanics and will benefit the field of mechanobiology.
Collapse
Affiliation(s)
- Yaqi Feng
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China.
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China.
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
16
|
Heo CH, Bak SY, Kim Y, Ok MR, Kim SY. Development of an integrin α v-based universal marker, capable of both prediction and direction of stem cell fate. Acta Biomater 2023; 166:291-300. [PMID: 37137404 DOI: 10.1016/j.actbio.2023.04.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/10/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023]
Abstract
Integrin-mediated focal adhesion (FA) and subsequent cytoskeletal reorganization influence cell morphology, migration, and ultimately cell fate. Previous studies have used various patterned surfaces with defined macroscopic cell shapes or nanoscopic FA distributions to explore how different substrates affect the fate of human bone marrow mesenchymal stem cells (BMSCs). However, there is currently no straightforward relationship between BMSC cell fates induced by patterned surfaces and FA distribution substrates. In this study, we conducted single-cell image analysis of integrin αv-mediated FA and cell morphological features of BMSCs during biochemically induced differentiation. This enabled the identification of distinct FA features that can discriminate between osteogenic and adipogenic differentiation, demonstrating that integrin αv-mediated focal adhesion (FA) can be used as a non-invasive biomarker for real time observation. Based on these results, we developed an organized microscale fibronectin (FN) patterned surface where the fate of BMSC could be precisely manipulated by these FA features. Notably, even in the absence of any biochemical inducers, such as those contained in the differentiation medium, BMSCs cultured on these FN patterned surfaces exhibited upregulation of differentiation markers comparable to BMSCs cultured using conventional differentiation methods. Therefore, the present study reveals the application of these FA features as universal markers not only for predicting differentiation status, but also for regulating cell fate by precisely controlling the FA features with a new cell culture platform. STATEMENT OF SIGNIFICANCE: Although the effects of material physiochemical properties on cell morphology and subsequent cell fate decisions have been extensively studied, a simple yet intuitive correlation between cellular features and differentiation remains unavailable. We present a single cell image-based strategy for predicting and directing stem cell fate. By using a specific integrin isoform, integrin αv, we identified distinct geometric features that can be used as a marker for discriminating between osteogenic and adipogenic differentiation in real-time. From these data, new cell culture platforms capable of regulating cell fate by precisely controlling FA features and cell area can be developed.
Collapse
Affiliation(s)
- Cheol Ho Heo
- Department of Applied Chemistry, Kookmin University, Seoul 02707, Republic of Korea
| | - Seon Young Bak
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Yonghan Kim
- Chemical and Biological Integrative Research Center, Biomedical Research Division, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Myoung-Ryul Ok
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul 02792, Republic of Korea.
| | - So Yeon Kim
- Chemical and Biological Integrative Research Center, Biomedical Research Division, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul 02792, Republic of Korea.
| |
Collapse
|
17
|
Zidane M, Makky A, Bruhns M, Rochwarger A, Babaei S, Claassen M, Schürch CM. A review on deep learning applications in highly multiplexed tissue imaging data analysis. FRONTIERS IN BIOINFORMATICS 2023; 3:1159381. [PMID: 37564726 PMCID: PMC10410935 DOI: 10.3389/fbinf.2023.1159381] [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: 02/05/2023] [Accepted: 07/12/2023] [Indexed: 08/12/2023] Open
Abstract
Since its introduction into the field of oncology, deep learning (DL) has impacted clinical discoveries and biomarker predictions. DL-driven discoveries and predictions in oncology are based on a variety of biological data such as genomics, proteomics, and imaging data. DL-based computational frameworks can predict genetic variant effects on gene expression, as well as protein structures based on amino acid sequences. Furthermore, DL algorithms can capture valuable mechanistic biological information from several spatial "omics" technologies, such as spatial transcriptomics and spatial proteomics. Here, we review the impact that the combination of artificial intelligence (AI) with spatial omics technologies has had on oncology, focusing on DL and its applications in biomedical image analysis, encompassing cell segmentation, cell phenotype identification, cancer prognostication, and therapy prediction. We highlight the advantages of using highly multiplexed images (spatial proteomics data) compared to single-stained, conventional histopathological ("simple") images, as the former can provide deep mechanistic insights that cannot be obtained by the latter, even with the aid of explainable AI. Furthermore, we provide the reader with the advantages/disadvantages of DL-based pipelines used in preprocessing highly multiplexed images (cell segmentation, cell type annotation). Therefore, this review also guides the reader to choose the DL-based pipeline that best fits their data. In conclusion, DL continues to be established as an essential tool in discovering novel biological mechanisms when combined with technologies such as highly multiplexed tissue imaging data. In balance with conventional medical data, its role in clinical routine will become more important, supporting diagnosis and prognosis in oncology, enhancing clinical decision-making, and improving the quality of care for patients. Since its introduction into the field of oncology, deep learning (DL) has impacted clinical discoveries and biomarker predictions. DL-driven discoveries and predictions in oncology are based on a variety of biological data such as genomics, proteomics, and imaging data. DL-based computational frameworks can predict genetic variant effects on gene expression, as well as protein structures based on amino acid sequences. Furthermore, DL algorithms can capture valuable mechanistic biological information from several spatial "omics" technologies, such as spatial transcriptomics and spatial proteomics. Here, we review the impact that the combination of artificial intelligence (AI) with spatial omics technologies has had on oncology, focusing on DL and its applications in biomedical image analysis, encompassing cell segmentation, cell phenotype identification, cancer prognostication, and therapy prediction. We highlight the advantages of using highly multiplexed images (spatial proteomics data) compared to single-stained, conventional histopathological ("simple") images, as the former can provide deep mechanistic insights that cannot be obtained by the latter, even with the aid of explainable AI. Furthermore, we provide the reader with the advantages/disadvantages of the DL-based pipelines used in preprocessing the highly multiplexed images (cell segmentation, cell type annotation). Therefore, this review also guides the reader to choose the DL-based pipeline that best fits their data. In conclusion, DL continues to be established as an essential tool in discovering novel biological mechanisms when combined with technologies such as highly multiplexed tissue imaging data. In balance with conventional medical data, its role in clinical routine will become more important, supporting diagnosis and prognosis in oncology, enhancing clinical decision-making, and improving the quality of care for patients.
Collapse
Affiliation(s)
- Mohammed Zidane
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Ahmad Makky
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Matthias Bruhns
- Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
- Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Alexander Rochwarger
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Sepideh Babaei
- Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
| | - Manfred Claassen
- Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
- Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Christian M. Schürch
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| |
Collapse
|
18
|
Peng M, Zhao Q, Wang M, Du X. Reconfigurable scaffolds for adaptive tissue regeneration. NANOSCALE 2023; 15:6105-6120. [PMID: 36919563 DOI: 10.1039/d3nr00281k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Tissue engineering and regenerative medicine have offered promising alternatives for clinical treatment of body tissue traumas, losses, dysfunctions, or diseases, where scaffold-based strategies are particularly popular and effective. Over the decades, scaffolds for tissue regeneration have been remarkably evolving. Nevertheless, conventional scaffolds still confront grand challenges in bio-adaptions in terms of both tissue-scaffold and cell-scaffold interplays, for example complying with complicated three-dimensional (3D) shapes of biological tissues and recapitulating the ordered cell regulation effects of native cell microenvironments. Benefiting from the recent advances in "intelligent" biomaterials, reconfigurable scaffolds have been emerging, demonstrating great promise in addressing the bio-adaption challenges through altering their macro-shapes and/or micro-structures. This mini-review article presents a brief overview of the cutting-edge research on reconfigurable scaffolds, summarizing the materials for forming reconfigurable scaffolds and highlighting their applications for adaptive tissue regeneration. Finally, the challenges and prospects of reconfigurable scaffolds are also discussed, shedding light on the bright future of next-generation reconfigurable scaffolds with upgrading adaptability.
Collapse
Affiliation(s)
- Mingxing Peng
- Institute of Biomedical & Health Engineering, Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen, 518055, China.
- University of Chinese Academy of Sciences, China
| | - Qilong Zhao
- Institute of Biomedical & Health Engineering, Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen, 518055, China.
| | - Min Wang
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Xuemin Du
- Institute of Biomedical & Health Engineering, Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen, 518055, China.
| |
Collapse
|
19
|
Kim SY, Ha SM, Kim DU, Park J, Park S, Hyun KA, Jung HI. Modularized dynamic cell culture platform for efficient production of extracellular vesicles and sequential analysis. LAB ON A CHIP 2023; 23:1852-1864. [PMID: 36825402 DOI: 10.1039/d2lc01129h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Extracellular vesicles (EVs) are nanometer-sized particles naturally secreted by cells for intercellular communication that encapsulate bioactive cargo, such as proteins and RNA, with a lipid bilayer. Tumor cell-derived EVs (tdEVs) are particularly promising biomarkers for cancer research because their contents reflect the cell of origin. In most studies, tdEVs have been obtained from cancer cells cultured under static conditions, thus lacking the ability to recapitulate the microenvironment of cells in vivo. Recent developments in perfusable cell culture systems have allowed oxygen and a nutrient gradient to mimic the physiological and cellular microenvironment. However, as these systems are perfused by circulating the culture medium within the unified structure, independently harvesting cells and EVs at each time point for analysis presents a limitation. In this study, a modularized cell culture system is designed for the perfusion and real-time collection of EVs. The system consists of three detachable chambers, one each for fresh medium, cell culture, and EV collection. The fresh medium flows from the medium chamber to the culture chamber at a flow rate controlled by the hydraulic pressure injected with a syringe pump. When the culture medium containing EVs exceeds a certain volume within the chamber, it overflows into the collection chamber to harvest EVs. The compact and modularized chambers are highly interoperable with conventional cell culture modalities used in the laboratory, thus enabling various EV-based assays.
Collapse
Affiliation(s)
- Seo Yeon Kim
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Republic of Korea.
| | - Seong Min Ha
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Republic of Korea.
| | - Dong-Uk Kim
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Republic of Korea.
| | - Junhyun Park
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Republic of Korea.
| | - Sunyoung Park
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Republic of Korea.
- The DABOM Inc., 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Republic of Korea
| | - Kyung-A Hyun
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Republic of Korea.
| | - Hyo-Il Jung
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Republic of Korea.
- The DABOM Inc., 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Republic of Korea
| |
Collapse
|
20
|
Skin Involved Nanotechnology. Nanomedicine (Lond) 2023. [DOI: 10.1007/978-981-16-8984-0_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
|
21
|
Shan Y, Zhang Q, Guo W, Wu Y, Miao Y, Xin H, Lian Q, Gu J. TIST: Transcriptome and Histopathological Image Integrative Analysis for Spatial Transcriptomics. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:974-988. [PMID: 36549467 PMCID: PMC10025771 DOI: 10.1016/j.gpb.2022.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 11/10/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022]
Abstract
Sequencing-based spatial transcriptomics (ST) is an emerging technology to study in situ gene expression patterns at the whole-genome scale. Currently, ST data analysis is still complicated by high technical noises and low resolution. In addition to the transcriptomic data, matched histopathological images are usually generated for the same tissue sample along the ST experiment. The matched high-resolution histopathological images provide complementary cellular phenotypical information, providing an opportunity to mitigate the noises in ST data. We present a novel ST data analysis method called transcriptome and histopathological image integrative analysis for ST (TIST), which enables the identification of spatial clusters (SCs) and the enhancement of spatial gene expression patterns by integrative analysis of matched transcriptomic data and images. TIST devises a histopathological feature extraction method based on Markov random field (MRF) to learn the cellular features from histopathological images, and integrates them with the transcriptomic data and location information as a network, termed TIST-net. Based on TIST-net, SCs are identified by a random walk-based strategy, and gene expression patterns are enhanced by neighborhood smoothing. We benchmark TIST on both simulated datasets and 32 real samples against several state-of-the-art methods. Results show that TIST is robust to technical noises on multiple analysis tasks for sequencing-based ST data and can find interesting microstructures in different biological scenarios. TIST is available at http://lifeome.net/software/tist/ and https://ngdc.cncb.ac.cn/biocode/tools/BT007317.
Collapse
Affiliation(s)
- Yiran Shan
- MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Qian Zhang
- MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Wenbo Guo
- MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Yanhong Wu
- MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Yuxin Miao
- MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Hongyi Xin
- UM-SJTU Joint Institute, Shanghai Jiao Tong University, Shanghai 200240, China; Department of Automation, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiuyu Lian
- UM-SJTU Joint Institute, Shanghai Jiao Tong University, Shanghai 200240, China; Department of Automation, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Jin Gu
- MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
22
|
Cesario A, D’Oria M, Simone I, Patarnello S, Valentini V, Scambia G. Open Innovation as the Catalyst in the Personalized Medicine to Personalized Digital Medicine Transition. J Pers Med 2022; 12:jpm12091500. [PMID: 36143285 PMCID: PMC9505138 DOI: 10.3390/jpm12091500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
Personalized medicine (PM) bridges several disciplines for understanding and addressing prevalent, complex, or rare situations in human health (e.g., complex phenotyping, risk stratification, etc.); therefore, digital and technological solutions have been integrated in the field to boost innovation and new knowledge generation. The open innovation (OI) paradigm proposes a method by which to respectfully manage disruptive change in biomedical organizations, as experienced by many organizations during digital transformation and the COVID-19 pandemic. In this article, we focus on how this paradigm has catalyzed the transition from PM to personalized digital medicine in a large-volume research hospital. Methods, challenges, and results are discussed. This case study is an endeavor to confirm that OI strategies could help manage urgent needs from the healthcare environment, while achieving sustainability-oriented, accountable innovation.
Collapse
Affiliation(s)
- Alfredo Cesario
- Scientific Directorate, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00182 Rome, Italy
- Gemelli Digital Medicine & Health, 00182 Rome, Italy
- Gemelli Generator, Gemelli Science and Technology Park (G-STeP), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00182 Rome, Italy
| | - Marika D’Oria
- Scientific Directorate, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00182 Rome, Italy
- Correspondence:
| | - Irene Simone
- Scientific Directorate, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00182 Rome, Italy
- Gemelli Digital Medicine & Health, 00182 Rome, Italy
| | - Stefano Patarnello
- Gemelli Digital Medicine & Health, 00182 Rome, Italy
- Gemelli Generator, Gemelli Science and Technology Park (G-STeP), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00182 Rome, Italy
| | - Vincenzo Valentini
- Gemelli Digital Medicine & Health, 00182 Rome, Italy
- Gemelli Generator, Gemelli Science and Technology Park (G-STeP), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00182 Rome, Italy
- Department of Diagnostic Imaging, Radiation Oncology and Hematology, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00182 Rome, Italy
| | - Giovanni Scambia
- Scientific Directorate, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00182 Rome, Italy
| |
Collapse
|
23
|
Prittinen J, Zhou X, Bano F, Backman L, Danielson P. Microstructured collagen films for 3D corneal stroma modelling. Connect Tissue Res 2022; 63:443-452. [PMID: 34894951 DOI: 10.1080/03008207.2021.2007901] [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] [Indexed: 02/03/2023]
Abstract
PURPOSE/AIM Corneal injury is a major cause of impaired vision around the globe. The fine structure of the corneal stroma plays a pivotal role in the phenotype and behavior of the embedded cells during homeostasis and healing after trauma or infection. In order to study healing processes in the cornea, it is important to create culture systems that functionally mimic the natural environment. MATERIALS AND METHODS Collagen solution was vitrified on top of a grated film to achieve thin collagen films with parallel microgrooves. Keratocytes (corneal stromal cells) were cultured on the films either as a single layer or as stacked layers of films and cells. SEM and F-actin staining were used to analyze the pattern transference onto the collagen and the cell orientation on the films. Cell viability was analyzed with MTS and live/dead staining. Keratocytes, fibroblasts, and myofibroblasts were cultured to study the pattern's effect on phenotype. RESULTS A microstructured collagen film-based culture system that guides keratocytes (stromal cells) to their native, layerwise perpendicular orientation in 3D and that can support fibroblasts and myofibroblasts was created. The films are thin and transparent enough to observe cells at least three layers deep. The cells maintain viability in 2D and 3D cultures and the films can support fibroblast and myofibroblast phenotypes. CONCLUSIONS The films provide an easily reproducible stroma model that maintains high cell viability and improves the preservation of the keratocyte phenotype in keratocytes that are differentiated to fibroblasts.
Collapse
Affiliation(s)
- Juha Prittinen
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
| | - Xin Zhou
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
| | - Fouzia Bano
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Ludvig Backman
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden.,Department of Community Medicine and Rehabilitation, Umeå University, Umeå, Sweden
| | - Patrik Danielson
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden.,Department of Clinical Sciences, Ophthalmology, Umeå University, Umeå, Sweden
| |
Collapse
|
24
|
Wu D, Zhao L, Sui B, Tan L, Lu L, Mao X, Liao G, Shi S, Cao Y, Yang X, Kou X. An Appearance Data-Driven Model Visualizes Cell State and Predicts Mesenchymal Stem Cell Regenerative Capacity. SMALL METHODS 2022; 6:e2200087. [PMID: 35674483 DOI: 10.1002/smtd.202200087] [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: 01/20/2022] [Revised: 04/14/2022] [Indexed: 06/15/2023]
Abstract
Mesenchymal stem cells (MSCs) are widely used in treating various diseases. However, lack of a reliable evaluation approach to characterize the potency of MSCs has dampened their clinical applications. Here, a function-oriented mathematical model is established to evaluate and predict the regenerative capacity (RC) of MSCs. Processed by exhaustive testing, the model excavates four optimal fitted indices, including nucleus roundness, nucleus/cytoplasm ratio, side-scatter height, and ERK1/2 from the given index combinations. Notably, three of them except ERK1/2 are cell appearance-associated features. The predictive power of the model is validated via screening experiments of these indices by predicting the RC of newly enrolled and chemical inhibitor-treated MSCs. Further RNA-sequencing analysis reveals that cell appearance-based indices may serve as major indicators to visualize the results of integration-weighted signals in and out of cells and reflect MSC stemness. In general, this study proposes an appearance data-driven predictive model for the RC and stemness of MSCs.
Collapse
Affiliation(s)
- Di Wu
- Hospital of Stomatology, Guanghua School of Stomatology, South China Center of Craniofacial Stem Cell Research, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
- Hospital of Stomatology, Guanghua School of Stomatology, Department of Oral and Maxillofacial Surgery, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
- Hospital of Stomatology, Guanghua School of Stomatology, Department of Orthodontics, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Lu Zhao
- Hospital of Stomatology, Guanghua School of Stomatology, South China Center of Craniofacial Stem Cell Research, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Bingdong Sui
- Hospital of Stomatology, Guanghua School of Stomatology, South China Center of Craniofacial Stem Cell Research, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
- State Key Laboratory of Military Stomatology, National Clinical Research Center for Oral Diseases, Shaanxi International Joint Research Center for Oral Diseases, Center for Tissue Engineering, School of Stomatology, The Fourth Military Medical University, Xi'an, 710032, China
| | - Lingping Tan
- Hospital of Stomatology, Guanghua School of Stomatology, South China Center of Craniofacial Stem Cell Research, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Lu Lu
- Hospital of Stomatology, Guanghua School of Stomatology, South China Center of Craniofacial Stem Cell Research, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Xueli Mao
- Hospital of Stomatology, Guanghua School of Stomatology, South China Center of Craniofacial Stem Cell Research, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Guiqing Liao
- Hospital of Stomatology, Guanghua School of Stomatology, Department of Oral and Maxillofacial Surgery, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Songtao Shi
- Hospital of Stomatology, Guanghua School of Stomatology, South China Center of Craniofacial Stem Cell Research, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
- Key Laboratory of Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China
| | - Yang Cao
- Hospital of Stomatology, Guanghua School of Stomatology, Department of Orthodontics, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Xiaobao Yang
- School of Physics and Optoelectronics, South China University of Technology, Guangzhou, 510640, China
| | - Xiaoxing Kou
- Hospital of Stomatology, Guanghua School of Stomatology, South China Center of Craniofacial Stem Cell Research, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
- Key Laboratory of Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China
| |
Collapse
|
25
|
Zhang Y, Habibovic P. Delivering Mechanical Stimulation to Cells: State of the Art in Materials and Devices Design. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2110267. [PMID: 35385176 DOI: 10.1002/adma.202110267] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/19/2022] [Indexed: 06/14/2023]
Abstract
Biochemical signals, such as growth factors, cytokines, and transcription factors are known to play a crucial role in regulating a variety of cellular activities as well as maintaining the normal function of different tissues and organs. If the biochemical signals are assumed to be one side of the coin, the other side comprises biophysical cues. There is growing evidence showing that biophysical signals, and in particular mechanical cues, also play an important role in different stages of human life ranging from morphogenesis during embryonic development to maturation and maintenance of tissue and organ function throughout life. In order to investigate how mechanical signals influence cell and tissue function, tremendous efforts have been devoted to fabricating various materials and devices for delivering mechanical stimuli to cells and tissues. Here, an overview of the current state of the art in the design and development of such materials and devices is provided, with a focus on their design principles, and challenges and perspectives for future research directions are highlighted.
Collapse
Affiliation(s)
- Yonggang Zhang
- Department of Instructive Biomaterials Engineering, Maastricht University, MERLN Institute for Technology-Inspired Regenerative Medicine, Universiteitssingel 40, Maastricht, 6229 ER, The Netherlands
| | - Pamela Habibovic
- Department of Instructive Biomaterials Engineering, Maastricht University, MERLN Institute for Technology-Inspired Regenerative Medicine, Universiteitssingel 40, Maastricht, 6229 ER, The Netherlands
| |
Collapse
|
26
|
Shin MJ, Im SH, Kim W, Ahn H, Shin TJ, Chung HJ, Yoon DK. Recyclable Periodic Nanostructure Formed by Sublimable Liquid Crystals for Robust Cell Alignment. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:3765-3774. [PMID: 35302783 DOI: 10.1021/acs.langmuir.1c03359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We demonstrate a facile method to fabricate a recyclable cell-alignment scaffold using nanogrooves based on sublimable liquid crystal (LC) material. Randomly and uniaxially arranged smectic LC structures are obtained, followed by sublimation and recondensation processes, which directly produce periodic nanogrooves with dimensions of a couple of hundreds of nanometers. After treatment with osmium tetroxide (OsO4), the nanogroove can serve as a scaffold to efficiently induce directed cell growth without causing cytotoxicity, and it can be used repeatedly. Together, various cell types are applied to the nanogroove, proving the scaffold's broad applicability. Depending on the nanotopography of the LC structures, cells exhibit different morphologies and gene expression patterns, compared to cells on standard glass substrates, according to microscopic observation and qPCR. Furthermore, cell sheets can be formed, which consist of oriented cells that can be repeatedly formed and transferred to other substrates, while maintaining its organization. We believe that our cell-aligning scaffold may pave the way for the soft material field to bioengineering, which can involve fundamentals in cell behavior and function, as well as applications for regenerative medicine.
Collapse
Affiliation(s)
- Min Jeong Shin
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - San Hae Im
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Wantae Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyungju Ahn
- Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Republic of Korea
| | - Tae Joo Shin
- Graduate School of Semiconductor Materials and Devices Engineering, UNIST, Ulsan, 44919, Republic of Korea
| | - Hyun Jung Chung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Graduate School of Nanoscience and Technology, orea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Dong Ki Yoon
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Graduate School of Nanoscience and Technology, orea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| |
Collapse
|
27
|
Das A, Adhikary S, Roy Chowdhury A, Barui A. Leveraging substrate stiffness to promote stem cell asymmetric division via mechanotransduction-polarity protein axis and its Bayesian regression analysis. Rejuvenation Res 2022; 25:59-69. [PMID: 35316074 DOI: 10.1089/rej.2021.0039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Asymmetric division of stem cells is an evolutionarily conserved process in multicellular organisms responsible for maintaining cellular fate diversity. Symmetric-asymmetric division pattern of mesenchymal stem cells (MSC) is regulated by both biochemical and biophysical cues. However, modulation of mechanotransduction pathway by varying scaffold properties and their adaptation to control stem cell division fate is not widely established. In present study, we explored the interplay between the mechanotrasduction pathway and polarity protein complex in stem cell asymmetry under varied biophysical stimuli. We hypothesize that variation of scaffold stiffness will impart mechanical stimulus and control the cytoskeleton assembly through RhoA, which will lead to further downstream activation of polarity-related cell signalling and asymmetric division of MSC. To establish the hypothesis, umbilical cord derived MSC were cultured on PCL/collagen scaffolds with varied stiffness and expressions of several important genes (viz. YAP, TAZ, LATS1, LATS2, Par3, Par6, PRKC1 (homolog of aPKC) and RhoA) and biomarkers (viz. YAP, TAZ, F-actin, Numb) were assessed. SVM polarity index was employed to understand the polarization status of the MSC cultured on varied scaffold stiffness. Further, the Bayesian logistic regression model was employed for classifying the asymmetric division of MSC cultured on different scaffold stiffness which showed 91% accuracy. Present study emphasizes the vital role of scaffold properties in modulating the mechanotransduction signalling pathway of MSC and provides mechanistic basis for adopting facile method to control stem cell division pattern towards improving tissue engineering outcome.
Collapse
Affiliation(s)
- Ankita Das
- Indian Institute of Engineering Science and Technology, 30130, Howrah, India;
| | - Shreya Adhikary
- Indian Institute of Engineering Science and Technology, 30130, Howrah, India;
| | - Amit Roy Chowdhury
- Indian Institute of Engineering Science and Technology, 30130, Howrah, India;
| | - Ananya Barui
- Indian Institute of Engineering Science and Technology, 30130, Centre for Healthcare science and Technology, IIEST Shibpur, Howrah, WB, Howrah, India, 711103;
| |
Collapse
|
28
|
Gao X, Wu Y, Cheng T, Stewart AG. Comprehensive multiplexed superfusion system enables physiological emulation in cell culture: exemplification by persistent circadian entrainment. LAB ON A CHIP 2022; 22:1137-1148. [PMID: 35199811 DOI: 10.1039/d1lc00841b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cells and tissues are routinely cultured in vitro for biological research with findings being extrapolated to their host organ and tissue function. However, most samples are cultured and studied in unphysiological environments, without temporal variation in the biochemical cues that are ubiquitous in vivo. The artificiality of these conditions undermines the predictive value of cell culture studies. We ascribe the prevalence of this suboptimal culture methodology to the lack of practical continuous flow systems that are economical and robust. Here, we design and implement an expandable multiplexed flow system for cell culture superfusion. By expanding on the concept of the planar peristaltic pump, we fabricated a highly compact and multiplexed pump head with up to 48 active pump lines. The pump is incorporated into a custom, open-top superfusion system configured for conventional multi-well culture plates. We then demonstrated the utility of the system for in vitro circadian entrainment using a daily cortisol pulse, generating a sustained circadian amplitude that is essential for physiological emulation and chrono-pharmacological studies. The multiplexed pump is complemented by a package of fluidic interconnection and management methods enabling user-friendly and scalable operation. Collectively, the suite of technologies provides a much-needed improvement in physiological emulation to support the predictive value of in vitro biomedical and biological research.
Collapse
Affiliation(s)
- Xumei Gao
- ARC Centre for Personalised Therapeutics Technologies, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Yanqi Wu
- ARC Centre for Personalised Therapeutics Technologies, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Biomedical Engineering, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Tianhong Cheng
- ARC Centre for Personalised Therapeutics Technologies, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Alastair G Stewart
- ARC Centre for Personalised Therapeutics Technologies, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC, 3010, Australia
| |
Collapse
|
29
|
Houthaeve G, De Smedt SC, Braeckmans K, De Vos WH. The cellular response to plasma membrane disruption for nanomaterial delivery. NANO CONVERGENCE 2022; 9:6. [PMID: 35103909 PMCID: PMC8807741 DOI: 10.1186/s40580-022-00298-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
Delivery of nanomaterials into cells is of interest for fundamental cell biological research as well as for therapeutic and diagnostic purposes. One way of doing so is by physically disrupting the plasma membrane (PM). Several methods that exploit electrical, mechanical or optical cues have been conceived to temporarily disrupt the PM for intracellular delivery, with variable effects on cell viability. However, apart from acute cytotoxicity, subtler effects on cell physiology may occur as well. Their nature and timing vary with the severity of the insult and the efficiency of repair, but some may provoke permanent phenotypic alterations. With the growing palette of nanoscale delivery methods and applications, comes a need for an in-depth understanding of this cellular response. In this review, we summarize current knowledge about the chronology of cellular events that take place upon PM injury inflicted by different delivery methods. We also elaborate on their significance for cell homeostasis and cell fate. Based on the crucial nodes that govern cell fitness and functionality, we give directions for fine-tuning nano-delivery conditions.
Collapse
Affiliation(s)
- Gaëlle Houthaeve
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ghent, Belgium
| | - Stefaan C De Smedt
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ghent, Belgium
| | - Winnok H De Vos
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium.
| |
Collapse
|
30
|
Lan Y, Huang N, Fu Y, Liu K, Zhang H, Li Y, Yang S. Morphology-Based Deep Learning Approach for Predicting Osteogenic Differentiation. Front Bioeng Biotechnol 2022; 9:802794. [PMID: 35155409 PMCID: PMC8830423 DOI: 10.3389/fbioe.2021.802794] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/30/2021] [Indexed: 02/03/2023] Open
Abstract
Early, high-throughput, and accurate recognition of osteogenic differentiation of stem cells is urgently required in stem cell therapy, tissue engineering, and regenerative medicine. In this study, we established an automatic deep learning algorithm, i.e., osteogenic convolutional neural network (OCNN), to quantitatively measure the osteogenic differentiation of rat bone marrow mesenchymal stem cells (rBMSCs). rBMSCs stained with F-actin and DAPI during early differentiation (day 0, 1, 4, and 7) were captured using laser confocal scanning microscopy to train OCNN. As a result, OCNN successfully distinguished differentiated cells at a very early stage (24 h) with a high area under the curve (AUC) (0.94 ± 0.04) and correlated with conventional biochemical markers. Meanwhile, OCNN exhibited better prediction performance compared with the single morphological parameters and support vector machine. Furthermore, OCNN successfully predicted the dose-dependent effects of small-molecule osteogenic drugs and a cytokine. OCNN-based online learning models can further recognize the osteogenic differentiation of rBMSCs cultured on several material surfaces. Hence, this study initially demonstrated the foreground of OCNN in osteogenic drug and biomaterial screening for next-generation tissue engineering and stem cell research.
Collapse
Affiliation(s)
- Yiqing Lan
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Nannan Huang
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Yiru Fu
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Kehao Liu
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - He Zhang
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Yuzhou Li
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
- *Correspondence: Yuzhou Li, ; Sheng Yang,
| | - Sheng Yang
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
- *Correspondence: Yuzhou Li, ; Sheng Yang,
| |
Collapse
|
31
|
Giergiel M, Zapotoczny B, Czyzynska-Cichon I, Konior J, Szymonski M. AFM image analysis of porous structures by means of neural networks. Biomed Signal Process Control 2022. [DOI: 10.1016/j.bspc.2021.103097] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
32
|
Skin Involved Nanotechnology. Nanomedicine (Lond) 2022. [DOI: 10.1007/978-981-13-9374-7_31-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
33
|
Skin Involved Nanotechnology. Nanomedicine (Lond) 2022. [DOI: 10.1007/978-981-13-9374-7_31-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
34
|
Dieterle MP, Husari A, Rolauffs B, Steinberg T, Tomakidi P. Integrins, cadherins and channels in cartilage mechanotransduction: perspectives for future regeneration strategies. Expert Rev Mol Med 2021; 23:e14. [PMID: 34702419 PMCID: PMC8724267 DOI: 10.1017/erm.2021.16] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 02/07/2023]
Abstract
Articular cartilage consists of hyaline cartilage, is a major constituent of the human musculoskeletal system and has critical functions in frictionless joint movement and articular homoeostasis. Osteoarthritis (OA) is an inflammatory disease of articular cartilage, which promotes joint degeneration. Although it affects millions of people, there are no satisfying therapies that address this disease at the molecular level. Therefore, tissue regeneration approaches aim at modifying chondrocyte biology to mitigate the consequences of OA. This requires appropriate biochemical and biophysical stimulation of cells. Regarding the latter, mechanotransduction of chondrocytes and their precursor cells has become increasingly important over the last few decades. Mechanotransduction is the transformation of external biophysical stimuli into intracellular biochemical signals, involving sensor molecules at the cell surface and intracellular signalling molecules, so-called mechano-sensors and -transducers. These signalling events determine cell behaviour. Mechanotransducing ion channels and gap junctions additionally govern chondrocyte physiology. It is of great scientific and medical interest to induce a specific cell behaviour by controlling these mechanotransduction pathways and to translate this knowledge into regenerative clinical therapies. This review therefore focuses on the mechanotransduction properties of integrins, cadherins and ion channels in cartilaginous tissues to provide perspectives for cartilage regeneration.
Collapse
Affiliation(s)
- Martin Philipp Dieterle
- Division of Oral Biotechnology, Center for Dental Medicine, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106Freiburg, Germany
| | - Ayman Husari
- Division of Oral Biotechnology, Center for Dental Medicine, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106Freiburg, Germany
- Department of Orthodontics, Center for Dental Medicine, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106Freiburg, Germany
| | - Bernd Rolauffs
- Department of Orthopedics and Trauma Surgery, G.E.R.N. Research Center for Tissue Replacement, Regeneration & Neogenesis, Medical Center – Albert-Ludwigs-University of Freiburg, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, 79085Freiburg im Breisgau, Germany
| | - Thorsten Steinberg
- Division of Oral Biotechnology, Center for Dental Medicine, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106Freiburg, Germany
| | - Pascal Tomakidi
- Division of Oral Biotechnology, Center for Dental Medicine, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106Freiburg, Germany
| |
Collapse
|
35
|
Harawaza K, Cousins B, Roach P, Fernandez A. Modification of the surface nanotopography of implant devices: A translational perspective. Mater Today Bio 2021; 12:100152. [PMID: 34746736 PMCID: PMC8554633 DOI: 10.1016/j.mtbio.2021.100152] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/16/2021] [Accepted: 10/19/2021] [Indexed: 01/24/2023] Open
Abstract
There is an increasing need for the development of superior, safe, and more sophisticated implants, especially as our society historically has been moving towards an increasingly aging population. Currently, most research is being focused on the next generation of advanced medical implants, that are not only biocompatible but have modified surfaces that direct specific immunomodulation at cellular level. While there is a plethora of information on cell-surface interaction and how surfaces can be nanofabricated at research level, less is known about how the academic knowledge has been translated into clinical trials and commercial technologies. In this review, we provide a clinical translational perspective on the use of controlled physical surface modification of medical implants, presenting an analysis of data acquired from clinical trials and commercial products. We also evaluate the state-of-the-art of nanofabrication techniques that are being applied for implant surface modification at a clinical level. Finally, we identify some current challenges in the field, including the need of more advanced nanopatterning techniques, the comparatively small number of clinical trials and comment on future avenues to be explored for a successful clinical translation.
Collapse
Affiliation(s)
- K. Harawaza
- Chemistry Department, School of Science, Loughborough University, Loughborough, LE11 3TU, UK
| | - B. Cousins
- Chemistry Department, School of Science, Loughborough University, Loughborough, LE11 3TU, UK
| | - P. Roach
- Chemistry Department, School of Science, Loughborough University, Loughborough, LE11 3TU, UK
| | - A. Fernandez
- Chemistry Department, School of Science, Loughborough University, Loughborough, LE11 3TU, UK
| |
Collapse
|
36
|
Mackay BS, Marshall K, Grant-Jacob JA, Kanczler J, Eason RW, Oreffo ROC, Mills B. The future of bone regeneration: integrating AI into tissue engineering. Biomed Phys Eng Express 2021; 7. [PMID: 34271556 DOI: 10.1088/2057-1976/ac154f] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/16/2021] [Indexed: 01/16/2023]
Abstract
Tissue engineering is a branch of regenerative medicine that harnesses biomaterial and stem cell research to utilise the body's natural healing responses to regenerate tissue and organs. There remain many unanswered questions in tissue engineering, with optimal biomaterial designs still to be developed and a lack of adequate stem cell knowledge limiting successful application. Advances in artificial intelligence (AI), and deep learning specifically, offer the potential to improve both scientific understanding and clinical outcomes in regenerative medicine. With enhanced perception of how to integrate artificial intelligence into current research and clinical practice, AI offers an invaluable tool to improve patient outcome.
Collapse
Affiliation(s)
- Benita S Mackay
- Optoelectronics Research Centre, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Karen Marshall
- Bone and Joint Research Group, Centre for Human Development, Stem Cells and Regeneration, Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO16 6HW, United Kingdom
| | - James A Grant-Jacob
- Optoelectronics Research Centre, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Janos Kanczler
- Bone and Joint Research Group, Centre for Human Development, Stem Cells and Regeneration, Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO16 6HW, United Kingdom
| | - Robert W Eason
- Optoelectronics Research Centre, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom.,Institute of Developmental Sciences, Faculty of Life Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Richard O C Oreffo
- Bone and Joint Research Group, Centre for Human Development, Stem Cells and Regeneration, Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO16 6HW, United Kingdom.,Institute of Developmental Sciences, Faculty of Life Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Ben Mills
- Optoelectronics Research Centre, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| |
Collapse
|
37
|
Mohindra P, Desai TA. Micro- and nanoscale biophysical cues for cardiovascular disease therapy. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2021; 34:102365. [PMID: 33571682 PMCID: PMC8217090 DOI: 10.1016/j.nano.2021.102365] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/15/2021] [Indexed: 11/19/2022]
Abstract
After cardiovascular injury, numerous pathological processes adversely impact the homeostatic function of cardiomyocyte, macrophage, fibroblast, endothelial cell, and vascular smooth muscle cell populations. Subsequent malfunctioning of these cells may further contribute to cardiovascular disease onset and progression. By modulating cellular responses after injury, it is possible to create local environments that promote wound healing and tissue repair mechanisms. The extracellular matrix continuously provides these mechanosensitive cell types with physical cues spanning the micro- and nanoscale to influence behaviors such as adhesion, morphology, and phenotype. It is therefore becoming increasingly compelling to harness these cell-substrate interactions to elicit more native cell behaviors that impede cardiovascular disease progression and enhance regenerative potential. This review discusses recent in vitro and preclinical work that have demonstrated the therapeutic implications of micro- and nanoscale biophysical cues on cell types adversely affected in cardiovascular diseases - cardiomyocytes, macrophages, fibroblasts, endothelial cells, and vascular smooth muscle cells.
Collapse
Affiliation(s)
- Priya Mohindra
- UC Berkeley-UCSF Graduate Program in Bioengineering, San Francisco, CA, United States
| | - Tejal A Desai
- UC Berkeley-UCSF Graduate Program in Bioengineering, San Francisco, CA, United States; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA.
| |
Collapse
|
38
|
Simionato G, Hinkelmann K, Chachanidze R, Bianchi P, Fermo E, van Wijk R, Leonetti M, Wagner C, Kaestner L, Quint S. Red blood cell phenotyping from 3D confocal images using artificial neural networks. PLoS Comput Biol 2021; 17:e1008934. [PMID: 33983926 PMCID: PMC8118337 DOI: 10.1371/journal.pcbi.1008934] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 04/01/2021] [Indexed: 12/15/2022] Open
Abstract
The investigation of cell shapes mostly relies on the manual classification of 2D images, causing a subjective and time consuming evaluation based on a portion of the cell surface. We present a dual-stage neural network architecture for analyzing fine shape details from confocal microscopy recordings in 3D. The system, tested on red blood cells, uses training data from both healthy donors and patients with a congenital blood disease, namely hereditary spherocytosis. Characteristic shape features are revealed from the spherical harmonics spectrum of each cell and are automatically processed to create a reproducible and unbiased shape recognition and classification. The results show the relation between the particular genetic mutation causing the disease and the shape profile. With the obtained 3D phenotypes, we suggest our method for diagnostics and theragnostics of blood diseases. Besides the application employed in this study, our algorithms can be easily adapted for the 3D shape phenotyping of other cell types and extend their use to other applications, such as industrial automated 3D quality control.
Collapse
Affiliation(s)
- Greta Simionato
- Department of Experimental Physics, Saarland University, Campus E2.6, Saarbrücken, Germany
- Institute for Clinical and Experimental Surgery, Saarland University, Campus University Hospital, Homburg, Germany
| | - Konrad Hinkelmann
- Department of Experimental Physics, Saarland University, Campus E2.6, Saarbrücken, Germany
| | - Revaz Chachanidze
- Department of Experimental Physics, Saarland University, Campus E2.6, Saarbrücken, Germany
- CNRS, University Grenoble Alpes, Grenoble INP, LRP, Grenoble, France
| | - Paola Bianchi
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Elisa Fermo
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Richard van Wijk
- Department of Clinical Chemistry & Haematology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marc Leonetti
- CNRS, University Grenoble Alpes, Grenoble INP, LRP, Grenoble, France
| | - Christian Wagner
- Department of Experimental Physics, Saarland University, Campus E2.6, Saarbrücken, Germany
- Physics and Materials Science Research Unit, University of Luxembourg, Luxembourg City, Luxembourg
| | - Lars Kaestner
- Department of Experimental Physics, Saarland University, Campus E2.6, Saarbrücken, Germany
- Theoretical Medicine and Biosciences, Saarland University, Campus University Hospital, Homburg, Germany
| | - Stephan Quint
- Department of Experimental Physics, Saarland University, Campus E2.6, Saarbrücken, Germany
- Cysmic GmbH, Saarland University, Saarbrücken, Germany
- * E-mail:
| |
Collapse
|
39
|
Li M, Xi N, Liu L. Peak force tapping atomic force microscopy for advancing cell and molecular biology. NANOSCALE 2021; 13:8358-8375. [PMID: 33913463 DOI: 10.1039/d1nr01303c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The advent of atomic force microscopy (AFM) provides an exciting tool to detect molecular and cellular behaviors under aqueous conditions. AFM is able to not only visualize the surface topography of the specimens, but also can quantify the mechanical properties of the specimens by force spectroscopy assay. Nevertheless, integrating AFM topographic imaging with force spectroscopy assay has long been limited due to the low spatiotemporal resolution. In recent years, the appearance of a new AFM imaging mode called peak force tapping (PFT) has shattered this limit. PFT allows AFM to simultaneously acquire the topography and mechanical properties of biological samples with unprecedented spatiotemporal resolution. The practical applications of PFT in the field of life sciences in the past decade have demonstrated the excellent capabilities of PFT in characterizing the fine structures and mechanics of living biological systems in their native states, offering novel possibilities to reveal the underlying mechanisms guiding physiological/pathological activities. In this paper, the recent progress in cell and molecular biology that has been made with the utilization of PFT is summarized, and future perspectives for further progression and biomedical applications of PFT are provided.
Collapse
Affiliation(s)
- Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China and Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China and University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ning Xi
- Department of Industrial and Manufacturing Systems Engineering, The University of Hong Kong, Hong Kong 999077, China
| | - Lianqing Liu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China and Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China and University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
40
|
Ma S, Zhao H, Galan EA. Integrating Engineering, Automation, and Intelligence to Catalyze the Biomedical Translation of Organoids. Adv Biol (Weinh) 2021; 5:e2100535. [PMID: 33984193 DOI: 10.1002/adbi.202100535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/21/2021] [Indexed: 12/13/2022]
Abstract
Organoid technology has developed at an impressive speed during the past decade. Still, organoids are not widely used in practical applications as expected. It is believed that this translation can be greatly accelerated with the integration of engineering and artificial intelligence into current research practices. It is proposed that this approach is the missing link to realize key milestones in organoid technology, namely, high-throughput, homogeneous, and standardized production, automated manipulation, and intelligent monitoring, evaluation, and control via integrated on-chip instrumentation and artificial intelligence. It is suggested that organoids-on-a-chip are the ideal platform to achieve these feats. Once these techniques are established and adopted by the scientific community, the rapid translation of organoids may be seen from laboratories to the clinics and pharmaceutical industry.
Collapse
Affiliation(s)
- Shaohua Ma
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen, 518055, China
| | - Haoran Zhao
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen, 518055, China
| | - Edgar A Galan
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen, 518055, China
| |
Collapse
|
41
|
Gavazzo P, Viti F, Donnelly H, Oliva MAG, Salmeron-Sanchez M, Dalby MJ, Vassalli M. Biophysical phenotyping of mesenchymal stem cells along the osteogenic differentiation pathway. Cell Biol Toxicol 2021; 37:915-933. [PMID: 33420657 DOI: 10.1007/s10565-020-09569-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/30/2020] [Indexed: 12/22/2022]
Abstract
Mesenchymal stem cells represent an important resource, for bone regenerative medicine and therapeutic applications. This review focuses on new advancements and biophysical tools which exploit different physical and chemical markers of mesenchymal stem cell populations, to finely characterize phenotype changes along their osteogenic differentiation process. Special attention is paid to recently developed label-free methods, which allow monitoring cell populations with minimal invasiveness. Among them, quantitative phase imaging, suitable for single-cell morphometric analysis, and nanoindentation, functional to cellular biomechanics investigation. Moreover, the pool of ion channels expressed in cells during differentiation is discussed, with particular interest for calcium homoeostasis.Altogether, a biophysical perspective of osteogenesis is proposed, offering a valuable tool for the assessment of the cell stage, but also suggesting potential physiological links between apparently independent phenomena.
Collapse
Affiliation(s)
- Paola Gavazzo
- Institute of Biophysics, National Research Council, Genoa, Italy
| | - Federica Viti
- Institute of Biophysics, National Research Council, Genoa, Italy.
| | - Hannah Donnelly
- Centre for the Cellular Microenvironment, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Mariana Azevedo Gonzalez Oliva
- Centre for the Cellular Microenvironment, Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, UK
| | - Manuel Salmeron-Sanchez
- Centre for the Cellular Microenvironment, Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, UK
| | - Matthew J Dalby
- Centre for the Cellular Microenvironment, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Massimo Vassalli
- Centre for the Cellular Microenvironment, Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, UK
| |
Collapse
|
42
|
Pennacchio FA, Nastały P, Poli A, Maiuri P. Tailoring Cellular Function: The Contribution of the Nucleus in Mechanotransduction. Front Bioeng Biotechnol 2021; 8:596746. [PMID: 33490050 PMCID: PMC7820809 DOI: 10.3389/fbioe.2020.596746] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
Cells sense a variety of different mechanochemical stimuli and promptly react to such signals by reshaping their morphology and adapting their structural organization and tensional state. Cell reactions to mechanical stimuli arising from the local microenvironment, mechanotransduction, play a crucial role in many cellular functions in both physiological and pathological conditions. To decipher this complex process, several studies have been undertaken to develop engineered materials and devices as tools to properly control cell mechanical state and evaluate cellular responses. Recent reports highlight how the nucleus serves as an important mechanosensor organelle and governs cell mechanoresponse. In this review, we will introduce the basic mechanisms linking cytoskeleton organization to the nucleus and how this reacts to mechanical properties of the cell microenvironment. We will also discuss how perturbations of nucleus-cytoskeleton connections, affecting mechanotransduction, influence health and disease. Moreover, we will present some of the main technological tools used to characterize and perturb the nuclear mechanical state.
Collapse
Affiliation(s)
- Fabrizio A. Pennacchio
- FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
| | - Paulina Nastały
- FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
- Laboratory of Translational Oncology, Institute of Medical Biotechnology and Experimental Oncology, Medical University of Gdańsk, Gdańsk, Poland
| | - Alessandro Poli
- FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
| | - Paolo Maiuri
- FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
| |
Collapse
|
43
|
Liu L, He F, Yu Y, Wang Y. Application of FRET Biosensors in Mechanobiology and Mechanopharmacological Screening. Front Bioeng Biotechnol 2020; 8:595497. [PMID: 33240867 PMCID: PMC7680962 DOI: 10.3389/fbioe.2020.595497] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 10/19/2020] [Indexed: 12/15/2022] Open
Abstract
Extensive studies have shown that cells can sense and modulate the biomechanical properties of the ECM within their resident microenvironment. Thus, targeting the mechanotransduction signaling pathways provides a promising way for disease intervention. However, how cells perceive these mechanical cues of the microenvironment and transduce them into biochemical signals remains to be answered. Förster or fluorescence resonance energy transfer (FRET) based biosensors are a powerful tool that can be used in live-cell mechanotransduction imaging and mechanopharmacological drug screening. In this review, we will first introduce FRET principle and FRET biosensors, and then, recent advances on the integration of FRET biosensors and mechanobiology in normal and pathophysiological conditions will be discussed. Furthermore, we will summarize the current applications and limitations of FRET biosensors in high-throughput drug screening and the future improvement of FRET biosensors. In summary, FRET biosensors have provided a powerful tool for mechanobiology studies to advance our understanding of how cells and matrices interact, and the mechanopharmacological screening for disease intervention.
Collapse
Affiliation(s)
| | | | | | - Yingxiao Wang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States
| |
Collapse
|
44
|
Chen Y, Wang J, Li X, Hu N, Voelcker NH, Xie X, Elnathan R. Emerging Roles of 1D Vertical Nanostructures in Orchestrating Immune Cell Functions. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2001668. [PMID: 32844502 PMCID: PMC7461044 DOI: 10.1002/adma.202001668] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/16/2020] [Indexed: 05/07/2023]
Abstract
Engineered nano-bio cellular interfaces driven by 1D vertical nanostructures (1D-VNS) are set to prompt radical progress in modulating cellular processes at the nanoscale. Here, tuneable cell-VNS interfacial interactions are probed and assessed, highlighting the use of 1D-VNS in immunomodulation, and intracellular delivery into immune cells-both crucial in fundamental and translational biomedical research. With programmable topography and adaptable surface functionalization, 1D-VNS provide unique biophysical and biochemical cues to orchestrate innate and adaptive immunity, both ex vivo and in vivo. The intimate nanoscale cell-VNS interface leads to membrane penetration and cellular deformation, facilitating efficient intracellular delivery of diverse bioactive cargoes into hard-to-transfect immune cells. The unsettled interfacial mechanisms reported to be involved in VNS-mediated intracellular delivery are discussed. By identifying up-to-date progress and fundamental challenges of current 1D-VNS technology in immune-cell manipulation, it is hoped that this report gives timely insights for further advances in developing 1D-VNS as a safe, universal, and highly scalable platform for cell engineering and enrichment in advanced cancer immunotherapy such as chimeric antigen receptor-T therapy.
Collapse
Affiliation(s)
- Yaping Chen
- Monash Institute of Pharmaceutical SciencesMonash University381 Royal ParadeParkvilleVIC3052Australia
- Melbourne Centre for NanofabricationVictorian Node of the Australian National Fabrication Facility151 Wellington RoadClayton3168Australia
| | - Ji Wang
- The First Affiliated Hospital of Sun Yat‐sen UniversitySun Yat‐sen UniversityGuangzhou510006China
| | - Xiangling Li
- State Key Laboratory of Optoelectronic Materials and TechnologiesSchool of Electronics and Information TechnologySun Yat‐sen UniversityGuangzhou510006China
| | - Ning Hu
- State Key Laboratory of Optoelectronic Materials and TechnologiesSchool of Electronics and Information TechnologySun Yat‐sen UniversityGuangzhou510006China
| | - Nicolas H. Voelcker
- Monash Institute of Pharmaceutical SciencesMonash University381 Royal ParadeParkvilleVIC3052Australia
- Melbourne Centre for NanofabricationVictorian Node of the Australian National Fabrication Facility151 Wellington RoadClayton3168Australia
- Department of Materials Science and EngineeringMonash University22 Alliance LaneClaytonVIC3168Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)ClaytonVIC3168Australia
- INM‐Leibniz Institute for New MaterialsCampus D2 2Saarbrücken66123Germany
| | - Xi Xie
- The First Affiliated Hospital of Sun Yat‐sen UniversitySun Yat‐sen UniversityGuangzhou510006China
- State Key Laboratory of Optoelectronic Materials and TechnologiesSchool of Electronics and Information TechnologySun Yat‐sen UniversityGuangzhou510006China
| | - Roey Elnathan
- Monash Institute of Pharmaceutical SciencesMonash University381 Royal ParadeParkvilleVIC3052Australia
- Melbourne Centre for NanofabricationVictorian Node of the Australian National Fabrication Facility151 Wellington RoadClayton3168Australia
- Department of Materials Science and EngineeringMonash University22 Alliance LaneClaytonVIC3168Australia
| |
Collapse
|
45
|
Laux L, Cutiongco MFA, Gadegaard N, Jensen BS. Interactive machine learning for fast and robust cell profiling. PLoS One 2020; 15:e0237972. [PMID: 32915784 PMCID: PMC7485821 DOI: 10.1371/journal.pone.0237972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 08/07/2020] [Indexed: 01/22/2023] Open
Abstract
Automated profiling of cell morphology is a powerful tool for inferring cell function. However, this technique retains a high barrier to entry. In particular, configuring image processing parameters for optimal cell profiling is susceptible to cognitive biases and dependent on user experience. Here, we use interactive machine learning to identify the optimum cell profiling configuration that maximises quality of the cell profiling outcome. The process is guided by the user, from whom a rating of the quality of a cell profiling configuration is obtained. We use Bayesian optimisation, an established machine learning algorithm, to learn from this information and automatically recommend the next configuration to examine with the aim of maximising the quality of the processing or analysis. Compared to existing interactive machine learning tools that require domain expertise for per-class or per-pixel annotations, we rely on users’ explicit assessment of output quality of the cell profiling task at hand. We validated our interactive approach against the standard human trial-and-error scheme to optimise an object segmentation task using the standard software CellProfiler. Our toolkit enabled rapid optimisation of an object segmentation pipeline, increasing the quality of object segmentation over a pipeline optimised through trial-and-error. Users also attested to the ease of use and reduced cognitive load enabled by our machine learning strategy over the standard approach. We envision that our interactive machine learning approach can enhance the quality and efficiency of pipeline optimisation to democratise image-based cell profiling.
Collapse
Affiliation(s)
- Lisa Laux
- School of Computing Science, University of Glasgow, Glasgow, Scotland
| | - Marie F. A. Cutiongco
- School of Engineering, Biomedical Engineering, University of Glasgow, Glasgow, Scotland
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, England
| | - Nikolaj Gadegaard
- School of Engineering, Biomedical Engineering, University of Glasgow, Glasgow, Scotland
| | - Bjørn Sand Jensen
- School of Computing Science, University of Glasgow, Glasgow, Scotland
- * E-mail:
| |
Collapse
|
46
|
Wang Y, Armato U, Wu J. Targeting Tunable Physical Properties of Materials for Chronic Wound Care. Front Bioeng Biotechnol 2020; 8:584. [PMID: 32596229 PMCID: PMC7300298 DOI: 10.3389/fbioe.2020.00584] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/13/2020] [Indexed: 12/12/2022] Open
Abstract
Chronic wounds caused by infections, diabetes, and radiation exposures are becoming a worldwide growing medical burden. Recent progress highlighted the physical signals determining stem cell fates and bacterial resistance, which holds potential to achieve a better wound regeneration in situ. Nanoparticles (NPs) would benefit chronic wound healing. However, the cytotoxicity of the silver NPs (AgNPs) has aroused many concerns. This review targets the tunable physical properties (i.e., mechanical-, structural-, and size-related properties) of either dermal matrixes or wound dressings for chronic wound care. Firstly, we discuss the recent discoveries about the mechanical- and structural-related regulation of stem cells. Specially, we point out the currently undocumented influence of tunable mechanical and structural properties on either the fate of each cell type or the whole wound healing process. Secondly, we highlight novel dermal matrixes based on either natural tropoelastin or synthetic elastin-like recombinamers (ELRs) for providing elastic recoil and resilience to the wounded dermis. Thirdly, we discuss the application of wound dressings in terms of size-related properties (i.e., metal NPs, lipid NPs, polymeric NPs). Moreover, we highlight the cytotoxicity of AgNPs and propose the size-, dose-, and time-dependent solutions for reducing their cytotoxicity in wound care. This review will hopefully inspire the advanced design strategies of either dermal matrixes or wound dressings and their potential therapeutic benefits for chronic wounds.
Collapse
Affiliation(s)
- Yuzhen Wang
- Research Center for Tissue Repair and Regeneration Affiliated to the Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College, Beijing, China
- PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Beijing, China
- Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, China
- Department of Burn and Plastic Surgery, Air Force Hospital of PLA Central Theater Command, Datong, China
| | - Ubaldo Armato
- Histology and Embryology Section, Department of Surgery, Dentistry, Pediatrics and Gynecology, University of Verona Medical School Verona, Verona, Italy
- Department of Burn and Plastic Surgery, Second People's Hospital of Shenzhen, Shenzhen University, Shenzhen, China
| | - Jun Wu
- Department of Burn and Plastic Surgery, Second People's Hospital of Shenzhen, Shenzhen University, Shenzhen, China
| |
Collapse
|
47
|
Huethorst E, Cutiongco MF, Campbell FA, Saeed A, Love R, Reynolds PM, Dalby MJ, Gadegaard N. Customizable, engineered substrates for rapid screening of cellular cues. Biofabrication 2020; 12:025009. [PMID: 31783378 PMCID: PMC7655147 DOI: 10.1088/1758-5090/ab5d3f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Biophysical cues robustly direct cell responses and are thus important tools for
in vitro and translational biomedical applications. High
throughput platforms exploring substrates with varying physical properties are
therefore valuable. However, currently existing platforms are limited in
throughput, the biomaterials used, the capability to segregate between different
cues and the assessment of dynamic responses. Here we present a multiwell array
(3 × 8) made of a substrate engineered to present topography or rigidity cues
welded to a bottomless plate with a 96-well format. Both the patterns on the
engineered substrate and the well plate format can be easily customized,
permitting systematic and efficient screening of biophysical cues. To
demonstrate the broad range of possible biophysical cues examinable, we designed
and tested three multiwell arrays to influence cardiomyocyte, chondrocyte and
osteoblast function. Using the multiwell array, we were able to measure
different cell functionalities using analytical modalities such as live
microscopy, qPCR and immunofluorescence. We observed that grooves (5
μm in size) induced less variation in contractile function
of cardiomyocytes. Compared to unpatterned plastic, nanopillars with 127 nm
height, 100 nm diameter and 300 nm pitch enhanced matrix deposition,
chondrogenic gene expression and chondrogenic maintenance. High aspect ratio
pillars with an elastic shear modulus of 16 kPa mimicking the matrix found in
early stages of bone development improved osteogenic gene expression compared to
stiff plastic. We envisage that our bespoke multiwell array will accelerate the
discovery of relevant biophysical cues through improved throughput and
variety.
Collapse
Affiliation(s)
- Eline Huethorst
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, G12 8LT, United Kingdom. Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|