1
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Liu Y, Uttam S. Perspective on quantitative phase imaging to improve precision cancer medicine. JOURNAL OF BIOMEDICAL OPTICS 2024; 29:S22705. [PMID: 38584967 PMCID: PMC10996848 DOI: 10.1117/1.jbo.29.s2.s22705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/03/2024] [Accepted: 03/15/2024] [Indexed: 04/09/2024]
Abstract
Significance Quantitative phase imaging (QPI) offers a label-free approach to non-invasively characterize cellular processes by exploiting their refractive index based intrinsic contrast. QPI captures this contrast by translating refractive index associated phase shifts into intensity-based quantifiable data with nanoscale sensitivity. It holds significant potential for advancing precision cancer medicine by providing quantitative characterization of the biophysical properties of cells and tissue in their natural states. Aim This perspective aims to discuss the potential of QPI to increase our understanding of cancer development and its response to therapeutics. It also explores new developments in QPI methods towards advancing personalized cancer therapy and early detection. Approach We begin by detailing the technical advancements of QPI, examining its implementations across transmission and reflection geometries and phase retrieval methods, both interferometric and non-interferometric. The focus then shifts to QPI's applications in cancer research, including dynamic cell mass imaging for drug response assessment, cancer risk stratification, and in-vivo tissue imaging. Results QPI has emerged as a crucial tool in precision cancer medicine, offering insights into tumor biology and treatment efficacy. Its sensitivity to detecting nanoscale changes holds promise for enhancing cancer diagnostics, risk assessment, and prognostication. The future of QPI is envisioned in its integration with artificial intelligence, morpho-dynamics, and spatial biology, broadening its impact in cancer research. Conclusions QPI presents significant potential in advancing precision cancer medicine and redefining our approach to cancer diagnosis, monitoring, and treatment. Future directions include harnessing high-throughput dynamic imaging, 3D QPI for realistic tumor models, and combining artificial intelligence with multi-omics data to extend QPI's capabilities. As a result, QPI stands at the forefront of cancer research and clinical application in cancer care.
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Affiliation(s)
- Yang Liu
- University of Illinois Urbana-Champaign, Beckman Institute for Advanced Science and Technology, Cancer Center at Illinois, Department of Bioengineering, Department of Electrical and Computer Engineering, Urbana, Illinois, United States
- University of Pittsburgh, Departments of Medicine and Bioengineering, Pittsburgh, Pennsylvania, United States
| | - Shikhar Uttam
- University of Pittsburgh, Department of Computational and Systems Biology, Pittsburgh, Pennsylvania, United States
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2
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Kim H, Jun T, Lee H, Chae BG, Yoon M, Kim C. Deep-learning based 3D birefringence image generation using 2D multi-view holographic images. Sci Rep 2024; 14:9879. [PMID: 38684698 PMCID: PMC11059389 DOI: 10.1038/s41598-024-60023-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Refractive index stands as an inherent characteristic of a material, allowing non-invasive exploration of the three-dimensional (3D) interior of the material. Certain materials with different refractive indices produce a birefringence phenomenon in which incident light is split into two polarization components when it passes through the materials. Representative birefringent materials appear in calcite crystals, liquid crystals (LCs), biological tissues, silk fibers, polymer films, etc. If the internal 3D shape of these materials can be visually expressed through a non-invasive method, it can greatly contribute to the semiconductor, display industry, optical components and devices, and biomedical diagnosis. This paper introduces a novel approach employing deep learning to generate 3D birefringence images using multi-viewed holographic interference images. First, we acquired a set of multi-viewed holographic interference pattern images and a 3D volume image of birefringence directly from a polarizing DTT (dielectric tensor tomography)-based microscope system about each LC droplet sample. The proposed model was trained to generate the 3D volume images of birefringence using the two-dimensional (2D) interference pattern image set. Performance evaluations were conducted against the ground truth images obtained directly from the DTT microscopy. Visualization techniques were applied to describe the refractive index distribution in the generated 3D images of birefringence. The results show the proposed method's efficiency in generating the 3D refractive index distribution from multi-viewed holographic interference images, presenting a novel data-driven alternative to traditional methods from the DTT devices.
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Affiliation(s)
- Hakdong Kim
- Department of Digital Contents, Sejong University, Seoul, Korea
| | - Taeheul Jun
- Department of Software Convergence, Sejong University, Seoul, Korea
| | - Hyoung Lee
- Communication and Media Research Lab, ETRI, Daejeon, Korea
| | - Byung Gyu Chae
- Communication and Media Research Lab, ETRI, Daejeon, Korea
| | - MinSung Yoon
- Communication and Media Research Lab, ETRI, Daejeon, Korea.
| | - Cheongwon Kim
- Department of Software, Sejong University, Seoul, Korea.
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3
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Miller ADC, Chowdhury SP, Hanson HW, Linderman SK, Ghasemi HI, Miller WD, Morrissey MA, Richardson CD, Gardner BM, Mukherjee A. Engineering water exchange is a safe and effective method for magnetic resonance imaging in diverse cell types. J Biol Eng 2024; 18:30. [PMID: 38649904 PMCID: PMC11035135 DOI: 10.1186/s13036-024-00424-5] [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: 09/26/2023] [Accepted: 04/08/2024] [Indexed: 04/25/2024] Open
Abstract
Aquaporin-1 (Aqp1), a water channel, has garnered significant interest for cell-based medicine and in vivo synthetic biology due to its ability to be genetically encoded to produce magnetic resonance signals by increasing the rate of water diffusion in cells. However, concerns regarding the effects of Aqp1 overexpression and increased membrane diffusivity on cell physiology have limited its widespread use as a deep-tissue reporter. In this study, we present evidence that Aqp1 generates strong diffusion-based magnetic resonance signals without adversely affecting cell viability or morphology in diverse cell lines derived from mice and humans. Our findings indicate that Aqp1 overexpression does not induce ER stress, which is frequently associated with heterologous expression of membrane proteins. Furthermore, we observed that Aqp1 expression had no detrimental effects on native biological activities, such as phagocytosis, immune response, insulin secretion, and tumor cell migration in the analyzed cell lines. These findings should serve to alleviate any lingering safety concerns regarding the utilization of Aqp1 as a genetic reporter and should foster its broader application as a noninvasive reporter for in vivo studies.
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Affiliation(s)
- Austin D C Miller
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA, 93106, USA
| | - Soham P Chowdhury
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Hadley W Hanson
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA, 93106, USA
| | - Sarah K Linderman
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Hannah I Ghasemi
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Wyatt D Miller
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA, 93106, USA
| | - Meghan A Morrissey
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Chris D Richardson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Brooke M Gardner
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Arnab Mukherjee
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA, 93106, USA.
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA.
- Department of Bioengineering, University of California, Santa Barbara, CA, 93106, USA.
- Department of Chemistry, University of California, Santa Barbara, CA, 93106, USA.
- Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA.
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4
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Wang YY, Zhai WD, Wu C, Yang S, Gong XZ. Exploring contribution of phytoplankton cell death to settleable particulate organic carbon in the East China Sea in spring. MARINE POLLUTION BULLETIN 2024; 201:116197. [PMID: 38422827 DOI: 10.1016/j.marpolbul.2024.116197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
Phytoplankton's death contributes to marine settleable particulate organic matter (POM). In this study, we used laboratory cultivation of different algal species to identify a positive correlation between the cumulative number of dead algal cells and POC>75 (carbon content of the settleable POM). The contribution coefficient of cell death to POC>75 varied among different algal species. Additionally, the field survey and incubation experiment were conducted in the East China Sea (ECS) to explore the spatial-temporal correlation between phytoplankton death and POC>75. The results concluded that phytoplankton death was the main factor controlling POC>75. In the ECS, the relationship between the surface cumulative mass of POC>75 and the cumulative number of dead cells followed: Cumulative mass of POC>75(mg) = 0.487 × Cumulative number of dead cells (/104) + 0.069. This study provided a methodology to quantitatively explain the relationship between phytoplankton death and settleable POM.
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Affiliation(s)
- Yan-Yan Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Wei-Dong Zhai
- Frontier Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China.
| | - Chi Wu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Laboratory for Marine Mineral Resources, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Shu Yang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Xian-Zhe Gong
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
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5
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Pulfer A, Pizzagalli DU, Gagliardi PA, Hinderling L, Lopez P, Zayats R, Carrillo-Barberà P, Antonello P, Palomino-Segura M, Grädel B, Nicolai M, Giusti A, Thelen M, Gambardella LM, Murooka TT, Pertz O, Krause R, Gonzalez SF. Transformer-based spatial-temporal detection of apoptotic cell death in live-cell imaging. eLife 2024; 12:RP90502. [PMID: 38497754 PMCID: PMC10948145 DOI: 10.7554/elife.90502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024] Open
Abstract
Intravital microscopy has revolutionized live-cell imaging by allowing the study of spatial-temporal cell dynamics in living animals. However, the complexity of the data generated by this technology has limited the development of effective computational tools to identify and quantify cell processes. Amongst them, apoptosis is a crucial form of regulated cell death involved in tissue homeostasis and host defense. Live-cell imaging enabled the study of apoptosis at the cellular level, enhancing our understanding of its spatial-temporal regulation. However, at present, no computational method can deliver robust detection of apoptosis in microscopy timelapses. To overcome this limitation, we developed ADeS, a deep learning-based apoptosis detection system that employs the principle of activity recognition. We trained ADeS on extensive datasets containing more than 10,000 apoptotic instances collected both in vitro and in vivo, achieving a classification accuracy above 98% and outperforming state-of-the-art solutions. ADeS is the first method capable of detecting the location and duration of multiple apoptotic events in full microscopy timelapses, surpassing human performance in the same task. We demonstrated the effectiveness and robustness of ADeS across various imaging modalities, cell types, and staining techniques. Finally, we employed ADeS to quantify cell survival in vitro and tissue damage in mice, demonstrating its potential application in toxicity assays, treatment evaluation, and inflammatory dynamics. Our findings suggest that ADeS is a valuable tool for the accurate detection and quantification of apoptosis in live-cell imaging and, in particular, intravital microscopy data, providing insights into the complex spatial-temporal regulation of this process.
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Affiliation(s)
- Alain Pulfer
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, USILuganoSwitzerland
- Department of Information Technology and Electrical Engineering, ETH ZurichZürichSwitzerland
| | - Diego Ulisse Pizzagalli
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, USILuganoSwitzerland
- Euler Institute, USILuganoSwitzerland
| | | | | | | | | | - Pau Carrillo-Barberà
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, USILuganoSwitzerland
- Instituto de Biotecnología y Biomedicina (BioTecMed), Universitat de ValènciaValenciaSpain
| | - Paola Antonello
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, USILuganoSwitzerland
- Institute of Cell Biology, University of BernBernSwitzerland
| | | | - Benjamin Grädel
- Institute of Cell Biology, University of BernBernSwitzerland
| | | | - Alessandro Giusti
- Dalle Molle Institute for Artificial Intelligence, IDSIALuganoSwitzerland
| | - Marcus Thelen
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, USILuganoSwitzerland
| | | | | | - Olivier Pertz
- Institute of Cell Biology, University of BernBernSwitzerland
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6
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Miller ADC, Chowdhury SP, Hanson HW, Linderman SK, Ghasemi HI, Miller WD, Morrissey MA, Richardson CD, Gardner BM, Mukherjee A. Engineering water exchange is a safe and effective method for magnetic resonance imaging in diverse cell types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.566095. [PMID: 37986852 PMCID: PMC10659288 DOI: 10.1101/2023.11.07.566095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Aquaporin-1 (Aqp1), a water channel, has garnered significant interest for cell-based medicine and in vivo synthetic biology due to its ability to be genetically encoded to produce magnetic resonance signals by increasing the rate of water diffusion in cells. However, concerns regarding the effects of Aqp1 overexpression and increased membrane diffusivity on cell physiology have limited its widespread use as a deep-tissue reporter. In this study, we present evidence that Aqp1 generates strong diffusion-based magnetic resonance signals without adversely affecting cell viability or morphology in diverse cell lines derived from mice and humans. Our findings indicate that Aqp1 overexpression does not induce ER stress, which is frequently associated with heterologous expression of membrane proteins. Furthermore, we observed that Aqp1 expression had no detrimental effects on native biological activities, such as phagocytosis, immune response, insulin secretion, and tumor cell migration in the analyzed cell lines. These findings should serve to alleviate any lingering safety concerns regarding the utilization of Aqp1 as a genetic reporter and should foster its broader application as a noninvasive reporter for in vivo studies.
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Affiliation(s)
- Austin D C Miller
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA 93106, USA
| | - Soham P Chowdhury
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Hadley W Hanson
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA 93106, USA
| | - Sarah K Linderman
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Hannah I Ghasemi
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Wyatt D Miller
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA 93106, USA
| | - Meghan A Morrissey
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Chris D Richardson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Brooke M Gardner
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Arnab Mukherjee
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA 93106, USA
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
- Department of Bioengineering, University of California, Santa Barbara, CA 93106, USA
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
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7
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Huang S, Liu Y, Wang C, Xiang W, Wang N, Peng L, Jiang X, Zhang X, Fu Z. Strategies for Cartilage Repair in Osteoarthritis Based on Diverse Mesenchymal Stem Cells-Derived Extracellular Vesicles. Orthop Surg 2023; 15:2749-2765. [PMID: 37620876 PMCID: PMC10622303 DOI: 10.1111/os.13848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 08/26/2023] Open
Abstract
Osteoarthritis (OA) causes disability and significant economic and social burden. Cartilage injury is one of the main pathological features of OA, and is often manifested by excessive chondrocyte death, inflammatory response, abnormal bone metabolism, imbalance of extracellular matrix (ECM) metabolism, and abnormal vascular or nerve growth. Regrettably, due to the avascular nature of cartilage, its capacity to repair is notably limited. Mesenchymal stem cells-derived extracellular vesicles (MSCs-EVs) play a pivotal role in intercellular communication, presenting promising potential not only as early diagnostic biomarkers in OA but also as efficacious therapeutic strategy. MSCs-EVs were confirmed to play a therapeutic role in the pathological process of cartilage injury mentioned above. This paper comprehensively provides the functions and mechanisms of MSCs-EVs in cartilage repair.
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Affiliation(s)
- Shanjun Huang
- Orthopedics DepartmentThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouChina
| | - Yujiao Liu
- Orthopedics DepartmentThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouChina
| | - Chenglong Wang
- Orthopedics DepartmentThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouChina
| | - Wei Xiang
- Orthopedics DepartmentThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouChina
| | - Nianwu Wang
- Orthopedics DepartmentThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouChina
| | - Li Peng
- Orthopedics DepartmentThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouChina
| | - Xuanang Jiang
- Orthopedics DepartmentThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouChina
| | - Xiaomin Zhang
- Orthopedics DepartmentThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouChina
| | - Zhijiang Fu
- Orthopedics DepartmentThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouChina
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8
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Moldovan C, Onaciu A, Toma V, Munteanu RA, Gulei D, Moldovan AI, Stiufiuc GF, Feder RI, Cenariu D, Iuga CA, Stiufiuc RI. Current trends in luminescence-based assessment of apoptosis. RSC Adv 2023; 13:31641-31658. [PMID: 37908656 PMCID: PMC10613953 DOI: 10.1039/d3ra05809c] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023] Open
Abstract
Apoptosis, the most extensively studied type of cell death, is known to play a crucial role in numerous processes such as elimination of unwanted cells or cellular debris, growth, control of the immune system, and prevention of malignancies. Defective regulation of apoptosis can trigger various diseases and disorders including cancer, neurological conditions, autoimmune diseases and developmental disorders. Knowing the nuances of the cell death type induced by a compound can help decipher which therapy is more effective for specific diseases. The detection of apoptotic cells using classic methods has brought significant contribution over the years, but innovative methods are quickly emerging and allow more in-depth understanding of the mechanisms, aside from a simple quantification. Due to increased sensitivity, time efficiency, pathway specificity and negligible cytotoxicity, these innovative approaches have great potential for both in vitro and in vivo studies. This review aims to shed light on the importance of developing and using novel nanoscale methods as an alternative to the classic apoptosis detection techniques.
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Affiliation(s)
- Cristian Moldovan
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
- Department of Pharmaceutical Physics & Biophysics, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy Louis Pasteur Street No. 4-6 400349 Cluj-Napoca Romania
| | - Anca Onaciu
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Valentin Toma
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Raluca A Munteanu
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Diana Gulei
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Alin I Moldovan
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Gabriela F Stiufiuc
- Faculty of Physics, "Babes Bolyai" University Mihail Kogalniceanu Street No. 1 400084 Cluj-Napoca Romania
| | - Richard I Feder
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Diana Cenariu
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
| | - Cristina A Iuga
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
- Pharmaceutical Analysis, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy Louis Pasteur Street 6 Cluj-Napoca 400349 Romania
| | - Rares I Stiufiuc
- Medfuture-Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy Marinescu 23/Louis Pasteur Street No. 4-6 400337 Cluj-Napoca Romania +40-0726-34-02-78
- Department of Pharmaceutical Physics & Biophysics, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy Louis Pasteur Street No. 4-6 400349 Cluj-Napoca Romania
- TRANSCEND Research Center, Regional Institute of Oncology 700483 Iasi Romania
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9
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Zhang Z, Jin L, Liu L, Zhou M, Zhang X, Zhang L. The intricate relationship between autoimmunity disease and neutrophils death patterns: a love-hate story. Apoptosis 2023; 28:1259-1284. [PMID: 37486407 DOI: 10.1007/s10495-023-01874-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
Autoimmune diseases are pathological conditions that result from the misidentification of self-antigens in immune system, leading to host tissue damage and destruction. These diseases can affect different organs and systems, including the blood, joints, skin, and muscles. Despite the significant progress made in comprehending the underlying pathogenesis, the complete mechanism of autoimmune disease is still not entirely understood. In autoimmune diseases, the innate immunocytes are not functioning properly: they are either abnormally activated or physically disabled. As a vital member of innate immunocyte, neutrophils and their modes of death are influenced by the microenvironment of different autoimmune diseases due to their short lifespan and diverse death modes. Related to neutrophil death pathways, apoptosis is the most frequent cell death form of neutrophil non-lytic morphology, delayed or aberrant apoptosis may contribute to the development anti-neutrophil cytoplasmic antibodies (ANCA)-associated vasculitis (AAV). In addition, NETosis, necroptosis and pyroptosis which are parts of lytic morphology exacerbate disease progression through various mechanisms in autoimmune diseases. This review aims to summarize recent advancements in understanding neutrophil death modes in various autoimmune diseases and provide insights into the development of novel therapeutic approaches for autoimmune diseases.
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Affiliation(s)
- Ziwei Zhang
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, China
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Hefei, China
- Anti-Inflammatory Immune Drugs Collaborative Innovation Center, Hefei, Anhui Province, China
| | - Lin Jin
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, China
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Hefei, China
- Anti-Inflammatory Immune Drugs Collaborative Innovation Center, Hefei, Anhui Province, China
| | - Lianghu Liu
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, China
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Hefei, China
- Anti-Inflammatory Immune Drugs Collaborative Innovation Center, Hefei, Anhui Province, China
| | - Mengqi Zhou
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, China
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Hefei, China
- Anti-Inflammatory Immune Drugs Collaborative Innovation Center, Hefei, Anhui Province, China
| | - Xianzheng Zhang
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, China.
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Hefei, China.
- Anti-Inflammatory Immune Drugs Collaborative Innovation Center, Hefei, Anhui Province, China.
| | - Lingling Zhang
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, China.
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Hefei, China.
- Anti-Inflammatory Immune Drugs Collaborative Innovation Center, Hefei, Anhui Province, China.
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10
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Zhou Z, Zhang Y, Xia S, Chen X. Red-Light-Activatable AND-Gated Antitumor Immunosuppressant. Cells 2023; 12:2351. [PMID: 37830565 PMCID: PMC10571834 DOI: 10.3390/cells12192351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/14/2023] Open
Abstract
Immunosuppressants are emerging as promising candidates for cancer therapy with lower cytotoxicity compared to traditional chemotherapy drugs; yet, the intrinsic side effects such as immunosuppression remain a critical concern. Herein, we introduce a photoactivatable antitumor immunosuppressant called dmBODIPY-FTY720 (BF) that shows no cytotoxicity but can be temporally and locally activated by deep-red light illumination to induce tumor cell apoptosis. To further reduce potential side effects, we integrate BF with another classic photosensitizer called methylene blue (MB) that is activated under the same wavelength of deep-red light (>650 nm) and successfully establish a red-light-activatable AND Boolean logic gate through a mechanism that we found to be synergetic apoptotic induction. At further decreased dosages, deep-red light illumination does not induce cell death in the presence of either BF or MB, but significant cancer cell death is triggered in the presence of both drugs. Therefore, the dosage of BF is further reduced, which will be highly beneficial to minimize any potential side effects of BF. This AND-gated strategy has been successfully applied in vivo for effective suppression of hepatocarcinoma tumors in living mice.
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Affiliation(s)
- Ziqi Zhou
- Laboratory of Chemical Biology and Frontier Biotechnologies, The HIT Center for Life Sciences (HCLS), Harbin Institute of Technology (HIT), Harbin 150001, China; (Z.Z.); (Y.Z.)
- School of Life Science and Technology, Harbin Institute of Technology (HIT), Harbin 150001, China
| | - Yan Zhang
- Laboratory of Chemical Biology and Frontier Biotechnologies, The HIT Center for Life Sciences (HCLS), Harbin Institute of Technology (HIT), Harbin 150001, China; (Z.Z.); (Y.Z.)
- School of Life Science and Technology, Harbin Institute of Technology (HIT), Harbin 150001, China
| | - Simin Xia
- Laboratory of Chemical Biology and Frontier Biotechnologies, The HIT Center for Life Sciences (HCLS), Harbin Institute of Technology (HIT), Harbin 150001, China; (Z.Z.); (Y.Z.)
| | - Xi Chen
- Laboratory of Chemical Biology and Frontier Biotechnologies, The HIT Center for Life Sciences (HCLS), Harbin Institute of Technology (HIT), Harbin 150001, China; (Z.Z.); (Y.Z.)
- School of Life Science and Technology, Harbin Institute of Technology (HIT), Harbin 150001, China
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11
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Wang Y, Zhai WD, Wu C. Algal cell viability assessment: The role of environmental factors in phytoplankton population dynamics. MARINE POLLUTION BULLETIN 2023; 189:114743. [PMID: 36898274 DOI: 10.1016/j.marpolbul.2023.114743] [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: 08/11/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
The viability of algal cells is one of the most fundamental issues in marine ecological research. In this work, a method was designed to identify algal cell viability based on digital holography and deep learning, which divided algal cells into three categories: active, weak, and dead cells. This method was applied to measure algal cells in surface waters of the East China Sea in spring, revealing about 4.34 %-23.29 % weak cells and 3.98 %-19.47 % dead cells. Levels of nitrate and chlorophyll a were the main factors affecting the viability of algal cells. Furthermore, algal viability changes during the heating and cooling were observed in laboratory experiments: high temperatures led to an increase in weak algal cells. This may provide an explanation for why most harmful algal blooms occur in warming months. This study provided a novel insight into how to identify the viability of algal cells and understand their significance in the ocean.
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Affiliation(s)
- Yanyan Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Wei-Dong Zhai
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China.
| | - Chi Wu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Laboratory for Marine Mineral Resources, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China.
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12
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Trizna EY, Sinitca AM, Lyanova AI, Baidamshina DR, Zelenikhin PV, Kaplun DI, Kayumov AR, Bogachev MI. Brightfield vs Fluorescent Staining Dataset-A Test Bed Image Set for Machine Learning based Virtual Staining. Sci Data 2023; 10:160. [PMID: 36949058 PMCID: PMC10033900 DOI: 10.1038/s41597-023-02065-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/10/2023] [Indexed: 03/24/2023] Open
Abstract
Differential fluorescent staining is an effective tool widely adopted for the visualization, segmentation and quantification of cells and cellular substructures as a part of standard microscopic imaging protocols. Incompatibility of staining agents with viable cells represents major and often inevitable limitations to its applicability in live experiments, requiring extraction of samples at different stages of experiment increasing laboratory costs. Accordingly, development of computerized image analysis methodology capable of segmentation and quantification of cells and cellular substructures from plain monochromatic images obtained by light microscopy without help of any physical markup techniques is of considerable interest. The enclosed set contains human colon adenocarcinoma Caco-2 cells microscopic images obtained under various imaging conditions with different viable vs non-viable cells fractions. Each field of view is provided in a three-fold representation, including phase-contrast microscopy and two differential fluorescent microscopy images with specific markup of viable and non-viable cells, respectively, produced using two different staining schemes, representing a prominent test bed for the validation of image analysis methods.
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Affiliation(s)
- Elena Y Trizna
- Institute for Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008, Russia
| | - Aleksandr M Sinitca
- Centre for Digital Telecommunication Technologies, St. Petersburg Electrotechnical University "LETI", St. Petersburg, 197022, Russia
| | - Asya I Lyanova
- Centre for Digital Telecommunication Technologies, St. Petersburg Electrotechnical University "LETI", St. Petersburg, 197022, Russia
| | - Diana R Baidamshina
- Institute for Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008, Russia
| | - Pavel V Zelenikhin
- Institute for Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008, Russia
| | - Dmitrii I Kaplun
- Centre for Digital Telecommunication Technologies, St. Petersburg Electrotechnical University "LETI", St. Petersburg, 197022, Russia
| | - Airat R Kayumov
- Institute for Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008, Russia.
| | - Mikhail I Bogachev
- Institute for Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008, Russia.
- Centre for Digital Telecommunication Technologies, St. Petersburg Electrotechnical University "LETI", St. Petersburg, 197022, Russia.
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13
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Exosomes treating osteoarthritis: hope with challenge. Heliyon 2023; 9:e13152. [PMID: 36711315 PMCID: PMC9880404 DOI: 10.1016/j.heliyon.2023.e13152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/23/2023] Open
Abstract
Osteoarthritis (OA) has been proven as the second primary cause of pain and disability in the elderly population, impact patients both physically and mentally, as well as imposing a heavy burden on the global healthcare system. Current treatment methods, whether conservative or surgical, that aim at relieving symptoms can not delay or reverse the degenerative process in the structure. Scientists and clinicians are facing a revolution in OA treatment strategies. The emergence of exosomes brings hope for OA treatment based on pathology, which is attributed to its full potential in protecting chondrocytes from excessive death, alleviating inflammation, maintaining cartilage matrix metabolism, and regulating angiogenesis and subchondral bone remodeling. Therefore, we summarized the recent studies of exosomes in OA, aiming to comprehensively understand the functions and mechanisms of exosomes in OA treatment, which may provide direction and theoretical support for formulating therapeutic strategies in the future.
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14
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Zhang M, Lin Y, Chen R, Yu H, Li Y, Chen M, Dou C, Yin P, Zhang L, Tang P. Ghost messages: cell death signals spread. Cell Commun Signal 2023; 21:6. [PMID: 36624476 PMCID: PMC9830882 DOI: 10.1186/s12964-022-01004-0] [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: 09/29/2022] [Accepted: 11/24/2022] [Indexed: 01/11/2023] Open
Abstract
Cell death is a mystery in various forms. Whichever type of cell death, this is always accompanied by active or passive molecules release. The recent years marked the renaissance of the study of these molecules showing they can signal to and communicate with recipient cells and regulate physio- or pathological events. This review summarizes the defined forms of messages cells could spread while dying, the effects of these signals on the target tissue/cells, and how these types of communications regulate physio- or pathological processes. By doing so, this review hopes to identify major unresolved questions in the field, formulate new hypothesis worthy of further investigation, and when possible, provide references for the search of novel diagnostic/therapeutics agents. Video abstract.
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Affiliation(s)
- Mingming Zhang
- grid.414252.40000 0004 1761 8894Department of Orthopedics, Chinese PLA General Hospital, Beijing, 100853 People’s Republic of China ,National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, 100853 People’s Republic of China
| | - Yuan Lin
- grid.412463.60000 0004 1762 6325Department of Orthopedics, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001 Heilongjiang People’s Republic of China
| | - Ruijing Chen
- grid.414252.40000 0004 1761 8894Department of Orthopedics, Chinese PLA General Hospital, Beijing, 100853 People’s Republic of China ,National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, 100853 People’s Republic of China
| | - Haikuan Yu
- grid.414252.40000 0004 1761 8894Department of Orthopedics, Chinese PLA General Hospital, Beijing, 100853 People’s Republic of China ,National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, 100853 People’s Republic of China
| | - Yi Li
- grid.414252.40000 0004 1761 8894Department of Orthopedics, Chinese PLA General Hospital, Beijing, 100853 People’s Republic of China ,National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, 100853 People’s Republic of China
| | - Ming Chen
- grid.414252.40000 0004 1761 8894Department of Orthopedics, Chinese PLA General Hospital, Beijing, 100853 People’s Republic of China ,National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, 100853 People’s Republic of China
| | - Ce Dou
- grid.410570.70000 0004 1760 6682Department of Orthopedics, Southwest Hospital, Army Medical University, Chongqing, 400038 People’s Republic of China
| | - Pengbin Yin
- grid.414252.40000 0004 1761 8894Department of Orthopedics, Chinese PLA General Hospital, Beijing, 100853 People’s Republic of China ,National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, 100853 People’s Republic of China
| | - Licheng Zhang
- grid.414252.40000 0004 1761 8894Department of Orthopedics, Chinese PLA General Hospital, Beijing, 100853 People’s Republic of China ,National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, 100853 People’s Republic of China
| | - Peifu Tang
- grid.414252.40000 0004 1761 8894Department of Orthopedics, Chinese PLA General Hospital, Beijing, 100853 People’s Republic of China ,National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Beijing, 100853 People’s Republic of China
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15
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Lu J, Öfverstedt J, Lindblad J, Sladoje N. Is image-to-image translation the panacea for multimodal image registration? A comparative study. PLoS One 2022; 17:e0276196. [PMID: 36441754 PMCID: PMC9704666 DOI: 10.1371/journal.pone.0276196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 09/30/2022] [Indexed: 11/29/2022] Open
Abstract
Despite current advancement in the field of biomedical image processing, propelled by the deep learning revolution, multimodal image registration, due to its several challenges, is still often performed manually by specialists. The recent success of image-to-image (I2I) translation in computer vision applications and its growing use in biomedical areas provide a tempting possibility of transforming the multimodal registration problem into a, potentially easier, monomodal one. We conduct an empirical study of the applicability of modern I2I translation methods for the task of rigid registration of multimodal biomedical and medical 2D and 3D images. We compare the performance of four Generative Adversarial Network (GAN)-based I2I translation methods and one contrastive representation learning method, subsequently combined with two representative monomodal registration methods, to judge the effectiveness of modality translation for multimodal image registration. We evaluate these method combinations on four publicly available multimodal (2D and 3D) datasets and compare with the performance of registration achieved by several well-known approaches acting directly on multimodal image data. Our results suggest that, although I2I translation may be helpful when the modalities to register are clearly correlated, registration of modalities which express distinctly different properties of the sample are not well handled by the I2I translation approach. The evaluated representation learning method, which aims to find abstract image-like representations of the information shared between the modalities, manages better, and so does the Mutual Information maximisation approach, acting directly on the original multimodal images. We share our complete experimental setup as open-source (https://github.com/MIDA-group/MultiRegEval), including method implementations, evaluation code, and all datasets, for further reproducing and benchmarking.
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Affiliation(s)
- Jiahao Lu
- MIDA Group, Department of Information Technology, Uppsala University, Uppsala, Sweden
- IMAGE Section, Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Johan Öfverstedt
- MIDA Group, Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Joakim Lindblad
- MIDA Group, Department of Information Technology, Uppsala University, Uppsala, Sweden
- * E-mail:
| | - Nataša Sladoje
- MIDA Group, Department of Information Technology, Uppsala University, Uppsala, Sweden
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16
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Wu H, Souedet N, Jan C, Clouchoux C, Delzescaux T. A general deep learning framework for neuron instance segmentation based on Efficient UNet and morphological post-processing. Comput Biol Med 2022; 150:106180. [PMID: 36244305 DOI: 10.1016/j.compbiomed.2022.106180] [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: 05/23/2022] [Revised: 09/21/2022] [Accepted: 10/01/2022] [Indexed: 11/03/2022]
Abstract
Recent studies have demonstrated the superiority of deep learning in medical image analysis, especially in cell instance segmentation, a fundamental step for many biological studies. However, the excellent performance of the neural networks requires training on large, unbiased dataset and annotations, which is labor-intensive and expertise-demanding. This paper presents an end-to-end framework to automatically detect and segment NeuN stained neuronal cells on histological images using only point annotations. Unlike traditional nuclei segmentation with point annotation, we propose using point annotation and binary segmentation to synthesize pixel-level annotations. The synthetic masks are used as the ground truth to train the neural network, a U-Net-like architecture with a state-of-the-art network, EfficientNet, as the encoder. Validation results show the superiority of our model compared to other recent methods. In addition, we investigated multiple post-processing schemes and proposed an original strategy to convert the probability map into segmented instances using ultimate erosion and dynamic reconstruction. This approach is easy to configure and outperforms other classical post-processing techniques. This work aims to develop a robust and efficient framework for analyzing neurons using optical microscopic data, which can be used in preclinical biological studies and, more specifically, in the context of neurodegenerative diseases. Code is available at: https://github.com/MIRCen/NeuronInstanceSeg.
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Affiliation(s)
- Huaqian Wu
- CEA-CNRS-UMR 9199, MIRCen, Fontenay-aux-Roses, France
| | | | - Caroline Jan
- CEA-CNRS-UMR 9199, MIRCen, Fontenay-aux-Roses, France
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17
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Nguyen TL, Pradeep S, Judson-Torres RL, Reed J, Teitell MA, Zangle TA. Quantitative Phase Imaging: Recent Advances and Expanding Potential in Biomedicine. ACS NANO 2022; 16:11516-11544. [PMID: 35916417 PMCID: PMC10112851 DOI: 10.1021/acsnano.1c11507] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Quantitative phase imaging (QPI) is a label-free, wide-field microscopy approach with significant opportunities for biomedical applications. QPI uses the natural phase shift of light as it passes through a transparent object, such as a mammalian cell, to quantify biomass distribution and spatial and temporal changes in biomass. Reported in cell studies more than 60 years ago, ongoing advances in QPI hardware and software are leading to numerous applications in biology, with a dramatic expansion in utility over the past two decades. Today, investigations of cell size, morphology, behavior, cellular viscoelasticity, drug efficacy, biomass accumulation and turnover, and transport mechanics are supporting studies of development, physiology, neural activity, cancer, and additional physiological processes and diseases. Here, we review the field of QPI in biology starting with underlying principles, followed by a discussion of technical approaches currently available or being developed, and end with an examination of the breadth of applications in use or under development. We comment on strengths and shortcomings for the deployment of QPI in key biomedical contexts and conclude with emerging challenges and opportunities based on combining QPI with other methodologies that expand the scope and utility of QPI even further.
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18
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Liu Y, Xiao W, Zhang H, Xin L, Li X, Pan F. Chemotherapy drug potency assessment method of ovarian cancer cells by digital holography microscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:4370-4385. [PMID: 36032571 PMCID: PMC9408259 DOI: 10.1364/boe.465149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/03/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Drug potency assessment plays a crucial role in cancer chemotherapy. The selection of appropriate chemotherapy drugs can reduce the impact on the patient's physical condition and achieve a better therapeutic effect. Various methods have been used to achieve in vitro drug susceptibility assays, but there are few studies on calculating morphology and texture parameters quantitatively based on phase imaging for drug potency assessment. In this study, digital holography microscopy was used to get phase imaging of ovarian cancer cells after adding three different drugs, namely, Cisplatin, Adriamycin, and 5-fluorouracil. Based on the reconstructed phase imaging, four parameters of ovarian cancer cells changed with time, such as the average height, projected area, cluster shade, and entropy, were calculated. And the half-inhibitory concentration of cells under the effect of different drugs was calculated according to these four parameters. The half-inhibitory concentration, which can directly reflect the drug potency, is associated with the morphological and texture features extracted from phase images by numerical fitting. So, a new method for calculating the half-inhibitory concentration was proposed. The result shows that the morphological and texture feature parameters can be used to evaluate the sensitivity of ovarian cancer cells to different drugs by fitting the half-inhibitory concentration numerically. And the result provides a new idea for drug potency assessment methods before chemotherapy for ovarian cancer.
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Affiliation(s)
- Yakun Liu
- Key Laboratory of Precision Opto-mechatronics Technology, School of Instrumentation and Optoelectronic Engineering, Beihang University, Beijing 100191, China
| | - Wen Xiao
- Key Laboratory of Precision Opto-mechatronics Technology, School of Instrumentation and Optoelectronic Engineering, Beihang University, Beijing 100191, China
| | - Huanzhi Zhang
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing 100044, China
| | - Lu Xin
- Key Laboratory of Precision Opto-mechatronics Technology, School of Instrumentation and Optoelectronic Engineering, Beihang University, Beijing 100191, China
| | - Xiaoping Li
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing 100044, China
| | - Feng Pan
- Key Laboratory of Precision Opto-mechatronics Technology, School of Instrumentation and Optoelectronic Engineering, Beihang University, Beijing 100191, China
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19
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Peltanová B, Holcová Polanská H, Raudenská M, Balvan J, Navrátil J, Vičar T, Gumulec J, Čechová B, Kräter M, Guck J, Kalfeřt D, Grega M, Plzák J, Betka J, Masařík M. mRNA Subtype of Cancer-Associated Fibroblasts Significantly Affects Key Characteristics of Head and Neck Cancer Cells. Cancers (Basel) 2022; 14:2286. [PMID: 35565415 PMCID: PMC9102192 DOI: 10.3390/cancers14092286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 12/10/2022] Open
Abstract
Head and neck squamous cell carcinomas (HNSCC) belong among severe and highly complex malignant diseases showing a high level of heterogeneity and consequently also a variance in therapeutic response, regardless of clinical stage. Our study implies that the progression of HNSCC may be supported by cancer-associated fibroblasts (CAFs) in the tumour microenvironment (TME) and the heterogeneity of this disease may lie in the level of cooperation between CAFs and epithelial cancer cells, as communication between CAFs and epithelial cancer cells seems to be a key factor for the sustained growth of the tumour mass. In this study, we investigated how CAFs derived from tumours of different mRNA subtypes influence the proliferation of cancer cells and their metabolic and biomechanical reprogramming. We also investigated the clinicopathological significance of the expression of these metabolism-related genes in tissue samples of HNSCC patients to identify a possible gene signature typical for HNSCC progression. We found that the right kind of cooperation between cancer cells and CAFs is needed for tumour growth and progression, and only specific mRNA subtypes can support the growth of primary cancer cells or metastases. Specifically, during coculture, cancer cell colony supporting effect and effect of CAFs on cell stiffness of cancer cells are driven by the mRNA subtype of the tumour from which the CAFs are derived. The degree of colony-forming support is reflected in cancer cell glycolysis levels and lactate shuttle-related transporters.
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Affiliation(s)
- Barbora Peltanová
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (B.P.); (H.H.P.); (M.R.); (J.B.); (J.N.); (J.G.); (B.Č.)
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
| | - Hana Holcová Polanská
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (B.P.); (H.H.P.); (M.R.); (J.B.); (J.N.); (J.G.); (B.Č.)
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
| | - Martina Raudenská
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (B.P.); (H.H.P.); (M.R.); (J.B.); (J.N.); (J.G.); (B.Č.)
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 61300 Brno, Czech Republic
| | - Jan Balvan
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (B.P.); (H.H.P.); (M.R.); (J.B.); (J.N.); (J.G.); (B.Č.)
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
| | - Jiří Navrátil
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (B.P.); (H.H.P.); (M.R.); (J.B.); (J.N.); (J.G.); (B.Č.)
| | - Tomáš Vičar
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
| | - Jaromír Gumulec
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (B.P.); (H.H.P.); (M.R.); (J.B.); (J.N.); (J.G.); (B.Č.)
| | - Barbora Čechová
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (B.P.); (H.H.P.); (M.R.); (J.B.); (J.N.); (J.G.); (B.Č.)
| | - Martin Kräter
- Max Planck Institute for the Science of Light, Staudtstraße 2, 91058 Erlangen, Germany; (M.K.); (J.G.)
| | - Jochen Guck
- Max Planck Institute for the Science of Light, Staudtstraße 2, 91058 Erlangen, Germany; (M.K.); (J.G.)
| | - David Kalfeřt
- Department of Otorhinolaryngology and Head and Neck Surgery, First Faculty of Medicine, University Hospital Motol, Charles University, V Uvalu 84, 15006 Prague, Czech Republic; (D.K.); (J.P.); (J.B.)
| | - Marek Grega
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, University Hospital Motol, Charles University, V Uvalu 84, 15006 Prague, Czech Republic;
| | - Jan Plzák
- Department of Otorhinolaryngology and Head and Neck Surgery, First Faculty of Medicine, University Hospital Motol, Charles University, V Uvalu 84, 15006 Prague, Czech Republic; (D.K.); (J.P.); (J.B.)
| | - Jan Betka
- Department of Otorhinolaryngology and Head and Neck Surgery, First Faculty of Medicine, University Hospital Motol, Charles University, V Uvalu 84, 15006 Prague, Czech Republic; (D.K.); (J.P.); (J.B.)
| | - Michal Masařík
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (B.P.); (H.H.P.); (M.R.); (J.B.); (J.N.); (J.G.); (B.Č.)
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
- BIOCEV, First Faculty of Medicine, Charles University, Prumyslova 595, 25250 Vestec, Czech Republic
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20
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Öfverstedt J, Lindblad J, Sladoje N. Fast computation of mutual information in the frequency domain with applications to global multimodal image alignment. Pattern Recognit Lett 2022. [DOI: 10.1016/j.patrec.2022.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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21
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Hsieh HC, Lin PT, Sung KB. Characterization and identification of cell death dynamics by quantitative phase imaging. JOURNAL OF BIOMEDICAL OPTICS 2022; 27:046502. [PMID: 35484694 PMCID: PMC9047449 DOI: 10.1117/1.jbo.27.4.046502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
SIGNIFICANCE Investigating cell death dynamics at the single-cell level plays an essential role in biological research. Quantitative phase imaging (QPI), a label-free method without adverse effects of exogenous labels, has been widely used to image many types of cells under various conditions. However, the dynamics of QPI features during cell death have not been thoroughly characterized. AIM We aim to develop a label-free technique to quantitatively characterize single-cell dynamics of cellular morphology and intracellular mass distribution of cells undergoing apoptosis and necrosis. APPROACH QPI was used to capture time-lapse phase images of apoptotic, necrotic, and normal cells. The dynamics of morphological and QPI features during cell death were fitted by a sigmoid function to quantify both the extent and rate of changes. RESULTS The two types of cell death mainly differed from normal cells in the lower phase of the central region and differed from each other in the sharp nuclear boundary shown in apoptotic cells. CONCLUSIONS The proposed method characterizes the dynamics of cellular morphology and intracellular mass distributions, which could be applied to studying cells undergoing state transition such as drug response.
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Affiliation(s)
- Huai-Ching Hsieh
- National Taiwan University, Department of Life Science, Taipei, Taiwan
- National Taiwan University, Department of Electrical Engineering, Taipei, Taiwan
| | - Po-Ting Lin
- National Taiwan University, Graduate Institute of Biomedical Electronics and Bioinformatics, Taipei, Taiwan
| | - Kung-Bin Sung
- National Taiwan University, Department of Electrical Engineering, Taipei, Taiwan
- National Taiwan University, Graduate Institute of Biomedical Electronics and Bioinformatics, Taipei, Taiwan
- National Taiwan University, Molecular Imaging Center, Taipei, Taiwan
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22
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Kabir MA, Kharel A, Malla S, Kreis ZJ, Nath P, Wolfe JN, Hassan M, Kaur D, Sari-Sarraf H, Tiwari AK, Ray A. Automated detection of apoptotic versus nonapoptotic cell death using label-free computational microscopy. JOURNAL OF BIOPHOTONICS 2022; 15:e202100310. [PMID: 34936215 DOI: 10.1002/jbio.202100310] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/09/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Identification of cell death mechanisms, particularly distinguishing between apoptotic versus nonapoptotic pathways, is of paramount importance for a wide range of applications related to cell signaling, interaction with pathogens, therapeutic processes, drug discovery, drug resistance, and even pathogenesis of diseases like cancers and neurogenerative disease among others. Here, we present a novel high-throughput method of identifying apoptotic versus necrotic versus other nonapoptotic cell death processes, based on lensless digital holography. This method relies on identification of the temporal changes in the morphological features of mammalian cells, which are unique to each cell death processes. Different cell death processes were induced by known cytotoxic agents. A deep learning-based approach was used to automatically classify the cell death mechanism (apoptotic vs necrotic vs nonapoptotic) with more than 93% accuracy. This label free approach can provide a low cost (<$250) alternative to some of the currently available high content imaging-based screening tools.
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Affiliation(s)
- Md Alamgir Kabir
- Department of Physics and Astronomy, University of Toledo, Toledo, OH, USA
| | - Ashish Kharel
- Department of Electrical and Computer Science, University of Toledo, Toledo, OH, USA
| | - Saloni Malla
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, USA
| | | | - Peuli Nath
- Department of Physics and Astronomy, University of Toledo, Toledo, OH, USA
| | - Jared Neil Wolfe
- Department of Mechanical Engineering, University of Toledo, Toledo, OH, USA
| | - Marwa Hassan
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, USA
| | - Devinder Kaur
- Department of Electrical and Computer Science, University of Toledo, Toledo, OH, USA
| | - Hamed Sari-Sarraf
- Department of Electrical & Computer Engineering, Texas Tech University, Lubbock, TX, USA
| | - Amit K Tiwari
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, USA
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH, USA
| | - Aniruddha Ray
- Department of Physics and Astronomy, University of Toledo, Toledo, OH, USA
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23
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Live-dead assay on unlabeled cells using phase imaging with computational specificity. Nat Commun 2022; 13:713. [PMID: 35132059 PMCID: PMC8821584 DOI: 10.1038/s41467-022-28214-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 01/11/2022] [Indexed: 12/20/2022] Open
Abstract
Existing approaches to evaluate cell viability involve cell staining with chemical reagents. However, the step of exogenous staining makes these methods undesirable for rapid, nondestructive, and long-term investigation. Here, we present an instantaneous viability assessment of unlabeled cells using phase imaging with computation specificity. This concept utilizes deep learning techniques to compute viability markers associated with the specimen measured by label-free quantitative phase imaging. Demonstrated on different live cell cultures, the proposed method reports approximately 95% accuracy in identifying live and dead cells. The evolution of the cell dry mass and nucleus area for the labeled and unlabeled populations reveal that the chemical reagents decrease viability. The nondestructive approach presented here may find a broad range of applications, from monitoring the production of biopharmaceuticals to assessing the effectiveness of cancer treatments. Common methods for characterising cell viability involve cell staining with chemical reagents. Here the authors report a method for cell viability assessment that does not require labelling; this uses quantitative phase imaging combined with deep learning.
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24
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Gao QH, Wen B, Kang Y, Zhang WM. Pump-free microfluidic magnetic levitation approach for density-based cell characterization. Biosens Bioelectron 2022; 204:114052. [PMID: 35149454 DOI: 10.1016/j.bios.2022.114052] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/22/2022] [Accepted: 01/27/2022] [Indexed: 11/16/2022]
Abstract
Magnetic levitation (MagLev) provides a simple but promising method for density-based analysis and detection down to the individual cell level. However, each existing MagLev configuration for the single-cell density measurement, mainly consisting of a capillary (∼50 mm) placed between two magnets, yields a fairly low sample utilization because of no knowledge about the sample cells in the regions other than the limited microscope vision. Moreover, the quantitative analysis may be affected due to the unclearly defined measurement area, which is specifically associated with the uneven magnetization of magnets, cell size, degree of aggregation. In this work, we explore a pump-free microfluidic magnetic levitation approach for density-based cell characterization, enabling sensitive and effective cellular density measurement on small sample volumes. The microfluidic MagLev comprises a pump-free microfluidic chip placed between two ring magnets with like poles facing. With no external pumps, connectors or control facility, much smaller amounts of fluids (∼4 μL) could be driven automatically in the entire microchannel in 16 s. Based on the pump-free mechanism, unique density signatures of cells from different lineages (ARPE-19, HCT116, HeLa, HT1080, Huh7) are characterized by monitoring the levitation profiles. Furthermore, variation in density of A549 lung cancer cells subjected to a drug treatment are observed in our platform, allowing evaluation of the efficacy of the drug treatment at the individual cell level. Thereby, the proposed pump-free microfluidic MagLev platform, a low-cost, fully automatic and portable design for label-free density-based cell characterization, provides a universal detection tool that operates efficiently within small-volume environments.
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Affiliation(s)
- Qiu-Hua Gao
- State Key Laboratory of Mechanical System and Vibration, School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Baiqing Wen
- School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yani Kang
- School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Wen-Ming Zhang
- State Key Laboratory of Mechanical System and Vibration, School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
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25
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Zicha D. Addressing cancer invasion and cell motility with quantitative light microscopy. Sci Rep 2022; 12:1621. [PMID: 35102173 PMCID: PMC8803927 DOI: 10.1038/s41598-022-05307-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/10/2022] [Indexed: 12/24/2022] Open
Abstract
The incidence of death caused by cancer has been increasing worldwide. The growth of cancer cells is not the main problem. The majority of deaths are due to invasion and metastasis, where cancer cells actively spread from primary tumors. Our inbred rat model of spontaneous metastasis revealed dynamic phenotype changes in vitro correlating with the metastatic potential in vivo and led to a discovery of a metastasis suppressor, protein 4.1B, which affects their 2D motility on flat substrates. Subsequently, others confirmed 4.1B as metastasis suppressor using knock-out mice and patient data suggesting mechanism involving apoptosis. There is evidence that 2D motility may be differentially controlled to the 3D situation. Here we show that 4.1B affects cell motility in an invasion assay similarly to the 2D system, further supporting our original hypothesis that the role of 4.1B as metastasis suppressor is primarily mediated by its effect on motility. This is encouraging for the validity of the 2D analysis, and we propose Quantitative Phase Imaging with incoherent light source for rapid and accurate testing of cancer cell motility and growth to be of interest for personalized cancer treatment as illustrated in experiments measuring responses of human adenocarcinoma cells to selected chemotherapeutic drugs.
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Affiliation(s)
- Daniel Zicha
- CEITEC - Central European Institute of Technology, Brno University of Technology, Purkyňova 656/123, 612 00, Brno, Czech Republic.
- Institute of Physical Engineering, Faculty of Mechanical Engineering, Brno University of Technology, Technická 2, 616 69, Brno, Czech Republic.
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26
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Manohar K, Gupta RK, Gupta P, Saha D, Gare S, Sarkar R, Misra A, Giri L. FDA approved L-type channel blocker Nifedipine reduces cell death in hypoxic A549 cells through modulation of mitochondrial calcium and superoxide generation. Free Radic Biol Med 2021; 177:189-200. [PMID: 34666149 PMCID: PMC8520174 DOI: 10.1016/j.freeradbiomed.2021.08.245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 08/26/2021] [Accepted: 08/29/2021] [Indexed: 01/04/2023]
Abstract
As hypoxia is a major driver for the pathophysiology of COVID-19, it is crucial to characterize the hypoxic response at the cellular and molecular levels. In order to augment drug repurposing with the identification of appropriate molecular targets, investigations on therapeutics preventing hypoxic cell damage is required. In this work, we propose a hypoxia model based on alveolar lung epithelial cells line using chemical inducer, CoCl2 that can be used for testing calcium channel blockers (CCBs). Since recent studies suggested that CCBs may reduce the infectivity of SARS-Cov-2, we specifically select FDA approved calcium channel blocker, nifedipine for the study. First, we examined hypoxia-induced cell morphology and found a significant increase in cytosolic calcium levels, mitochondrial calcium overload as well as ROS production in hypoxic A549 cells. Secondly, we demonstrate the protective behaviour of nifedipine for cells that are already subjected to hypoxia through measurement of cell viability as well as 4D imaging of cellular morphology and nuclear condensation. Thirdly, we show that the protective effect of nifedipine is achieved through the reduction of cytosolic calcium, mitochondrial calcium, and ROS generation. Overall, we outline a framework for quantitative analysis of mitochondrial calcium and ROS using 3D imaging in laser scanning confocal microscopy and the open-source image analysis platform ImageJ. The proposed pipeline was used to visualize mitochondrial calcium and ROS level in individual cells that provide an understanding of molecular targets. Our findings suggest that the therapeutic value of nifedipine may potentially be evaluated in the context of COVID-19 therapeutic trials.
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Affiliation(s)
- Kuruba Manohar
- Department of Biotechnology, Indian Institute of Technology, Hyderabad, 502285, India
| | - Rishikesh Kumar Gupta
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, 02 109, Poland; Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, 02-091, Poland
| | - Parth Gupta
- Department of Biotechnology, Indian Institute of Technology, Hyderabad, 502285, India
| | - Debasmita Saha
- Department of Chemical Engineering, Indian Institute of Technology, Hyderabad, 502285, India
| | - Suman Gare
- Department of Chemical Engineering, Indian Institute of Technology, Hyderabad, 502285, India
| | - Rahuldeb Sarkar
- Departments of Respiratory Medicine and Critical Care, Medway NHS Foundation Trust, Gillingham, Kent, UK; Faculty of Life Sciences, King's College London, London, UK
| | - Ashish Misra
- Department of Biotechnology, Indian Institute of Technology, Hyderabad, 502285, India
| | - Lopamudra Giri
- Department of Chemical Engineering, Indian Institute of Technology, Hyderabad, 502285, India.
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27
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Wei J, Gao Y, Wang D, Zhang X, Fan S, Bao T, Gao X, Hu G, Wang A, Jia J. Discovery of Highly Oxidized Abietane Diterpenoids from the Roots of
Euphorbia fischeriana
with Anti‐tumor Activities. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jiang‐Chun Wei
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University Shenyang Liaoning 110016 China
| | - Yu‐Ning Gao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University Shenyang Liaoning 110016 China
| | - Dong‐Dong Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University Shenyang Liaoning 110016 China
| | - Xiao‐Yu Zhang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University Shenyang Liaoning 110016 China
| | - San‐Peng Fan
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University Shenyang Liaoning 110016 China
| | - Te‐Ri‐Gen Bao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University Shenyang Liaoning 110016 China
| | - Xiao‐Xu Gao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University Shenyang Liaoning 110016 China
| | - Gao‐Sheng Hu
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University Shenyang Liaoning 110016 China
| | - An‐Hua Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University Shenyang Liaoning 110016 China
| | - Jing‐Ming Jia
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University Shenyang Liaoning 110016 China
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28
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Saranya J, Sreeja BS, Arivanandan M, Bhuvaneswari K, Sherin S, Shivani KS, SaradhaPreetha G, Saroja KK. Nanoarchitectonics of Cerium Oxide/Zinc Oxide/Graphene Oxide Composites for Evaluation of Cytotoxicity and Apoptotic Behavior in HeLa and VERO Cell Lines. J Inorg Organomet Polym Mater 2021. [DOI: 10.1007/s10904-021-02128-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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29
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Macaque neuron instance segmentation only with point annotations based on multiscale fully convolutional regression neural network. Neural Comput Appl 2021. [DOI: 10.1007/s00521-021-06574-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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30
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Vicar T, Chmelik J, Jakubicek R, Chmelikova L, Gumulec J, Balvan J, Provaznik I, Kolar R. Self-supervised pretraining for transferable quantitative phase image cell segmentation. BIOMEDICAL OPTICS EXPRESS 2021; 12:6514-6528. [PMID: 34745753 PMCID: PMC8547997 DOI: 10.1364/boe.433212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/03/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
In this paper, a novel U-Net-based method for robust adherent cell segmentation for quantitative phase microscopy image is designed and optimised. We designed and evaluated four specific post-processing pipelines. To increase the transferability to different cell types, non-deep learning transfer with adjustable parameters is used in the post-processing step. Additionally, we proposed a self-supervised pretraining technique using nonlabelled data, which is trained to reconstruct multiple image distortions and improved the segmentation performance from 0.67 to 0.70 of object-wise intersection over union. Moreover, we publish a new dataset of manually labelled images suitable for this task together with the unlabelled data for self-supervised pretraining.
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Affiliation(s)
- Tomas Vicar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jiri Chmelik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Roman Jakubicek
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Larisa Chmelikova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Jaromir Gumulec
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jan Balvan
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Ivo Provaznik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Radim Kolar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
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31
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Kim DNH, Lim AA, Teitell MA. Rapid, label-free classification of tumor-reactive T cell killing with quantitative phase microscopy and machine learning. Sci Rep 2021; 11:19448. [PMID: 34593878 PMCID: PMC8484462 DOI: 10.1038/s41598-021-98567-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/08/2021] [Indexed: 11/08/2022] Open
Abstract
Quantitative phase microscopy (QPM) enables studies of living biological systems without exogenous labels. To increase the utility of QPM, machine-learning methods have been adapted to extract additional information from the quantitative phase data. Previous QPM approaches focused on fluid flow systems or time-lapse images that provide high throughput data for cells at single time points, or of time-lapse images that require delayed post-experiment analyses, respectively. To date, QPM studies have not imaged specific cells over time with rapid, concurrent analyses during image acquisition. In order to study biological phenomena or cellular interactions over time, efficient time-dependent methods that automatically and rapidly identify events of interest are desirable. Here, we present an approach that combines QPM and machine learning to identify tumor-reactive T cell killing of adherent cancer cells rapidly, which could be used for identifying and isolating novel T cells and/or their T cell receptors for studies in cancer immunotherapy. We demonstrate the utility of this method by machine learning model training and validation studies using one melanoma-cognate T cell receptor model system, followed by high classification accuracy in identifying T cell killing in an additional, independent melanoma-cognate T cell receptor model system. This general approach could be useful for studying additional biological systems under label-free conditions over extended periods of examination.
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Affiliation(s)
- Diane N H Kim
- Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA
| | - Alexander A Lim
- Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA
| | - Michael A Teitell
- Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA.
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, 90095, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA.
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, 90095, USA.
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA.
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
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32
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Belashov AV, Zhikhoreva AA, Belyaeva TN, Salova AV, Kornilova ES, Semenova IV, Vasyutinskii OS. Machine Learning Assisted Classification of Cell Lines and Cell States on Quantitative Phase Images. Cells 2021; 10:2587. [PMID: 34685568 PMCID: PMC8533984 DOI: 10.3390/cells10102587] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 12/20/2022] Open
Abstract
In this report, we present implementation and validation of machine-learning classifiers for distinguishing between cell types (HeLa, A549, 3T3 cell lines) and states (live, necrosis, apoptosis) based on the analysis of optical parameters derived from cell phase images. Validation of the developed classifier shows the accuracy for distinguishing between the three cell types of about 93% and between different cell states of the same cell line of about 89%. In the field test of the developed algorithm, we demonstrate successful evaluation of the temporal dynamics of relative amounts of live, apoptotic and necrotic cells after photodynamic treatment at different doses.
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Affiliation(s)
- Andrey V. Belashov
- Ioffe Institute, 26, Polytekhnicheskaya, 194021 St. Petersburg, Russia; (A.A.Z.); (I.V.S.); (O.S.V.)
| | - Anna A. Zhikhoreva
- Ioffe Institute, 26, Polytekhnicheskaya, 194021 St. Petersburg, Russia; (A.A.Z.); (I.V.S.); (O.S.V.)
| | - Tatiana N. Belyaeva
- Institute of Cytology of RAS, 4, Tikhoretsky pr., 194064 St. Petersburg, Russia; (T.N.B.); (A.V.S.); (E.S.K.)
| | - Anna V. Salova
- Institute of Cytology of RAS, 4, Tikhoretsky pr., 194064 St. Petersburg, Russia; (T.N.B.); (A.V.S.); (E.S.K.)
| | - Elena S. Kornilova
- Institute of Cytology of RAS, 4, Tikhoretsky pr., 194064 St. Petersburg, Russia; (T.N.B.); (A.V.S.); (E.S.K.)
- Institute for Biomedical Systems and Biotechnology, Peter the Great St. Petersburg Polytechnic University, 29, Polytekhnicheskaya, 195251 St. Petersburg, Russia
| | - Irina V. Semenova
- Ioffe Institute, 26, Polytekhnicheskaya, 194021 St. Petersburg, Russia; (A.A.Z.); (I.V.S.); (O.S.V.)
| | - Oleg S. Vasyutinskii
- Ioffe Institute, 26, Polytekhnicheskaya, 194021 St. Petersburg, Russia; (A.A.Z.); (I.V.S.); (O.S.V.)
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33
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SAP130 released by damaged tubule drives necroinflammation via miRNA-219c/Mincle signaling in acute kidney injury. Cell Death Dis 2021; 12:866. [PMID: 34556635 PMCID: PMC8460660 DOI: 10.1038/s41419-021-04131-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 08/14/2021] [Accepted: 08/26/2021] [Indexed: 12/30/2022]
Abstract
Tubules injury and immune cell activation are the common pathogenic mechanisms in acute kidney injury (AKI). However, the exact modes of immune cell activation following tubule damage are not fully understood. Here we uncovered that the release of cytoplasmic spliceosome associated protein 130 (SAP130) from the damaged tubular cells mediated necroinflammation by triggering macrophage activation via miRNA-219c(miR-219c)/Mincle-dependent mechanism in unilateral ureteral obstruction (UUO) and cisplatin-induced AKI mouse models, and in patients with acute tubule necrosis (ATN). In the AKI kidneys, we found that Mincle expression was tightly correlated to the necrotic tubular epithelial cells (TECs) with higher expression of SAP130, a damaged associated molecule pattern (DAMP), suggesting that SAP130 released from damaged tubular cells may trigger macrophage activation and necroinflammation. This was confirmed in vivo in which administration of SAP130-rich supernatant from dead TECs or recombinant SAP130 promoted Mincle expression and macrophage accumulation which became worsen with profound tubulointerstitial inflammation in LPS-primed Mincle WT mice but not in Mincle deficient mice. Further studies identified that Mincle was negatively regulated via miR-219c-3p in macrophages as miR-219c-3p bound Mincle 3′-UTR to inhibit Mincle translation. Besides, lentivirus-mediated renal miR-219c-3p overexpression blunted Mincle and proinflammatory cytokine expression as well as macrophage infiltration in the inflamed kidney of UUO mice. In conclusion, SAP130 is released by damaged tubules which elicit Mincle activation on macrophages and renal necroinflammation via the miR-219c-3p-dependent mechanism. Results from this study suggest that targeting miR-219c-3p/Mincle signaling may represent a novel therapy for AKI.
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34
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Verduijn J, Van der Meeren L, Krysko DV, Skirtach AG. Deep learning with digital holographic microscopy discriminates apoptosis and necroptosis. Cell Death Dis 2021; 7:229. [PMID: 34475384 PMCID: PMC8413278 DOI: 10.1038/s41420-021-00616-8] [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: 06/11/2021] [Revised: 08/13/2021] [Accepted: 08/19/2021] [Indexed: 02/07/2023]
Abstract
Regulated cell death modalities such as apoptosis and necroptosis play an important role in regulating different cellular processes. Currently, regulated cell death is identified using the golden standard techniques such as fluorescence microscopy and flow cytometry. However, they require fluorescent labels, which are potentially phototoxic. Therefore, there is a need for the development of new label-free methods. In this work, we apply Digital Holographic Microscopy (DHM) coupled with a deep learning algorithm to distinguish between alive, apoptotic and necroptotic cells in murine cancer cells. This method is solely based on label-free quantitative phase images, where the phase delay of light by cells is quantified and is used to calculate their topography. We show that a combination of label-free DHM in a high-throughput set-up (~10,000 cells per condition) can discriminate between apoptosis, necroptosis and alive cells in the L929sAhFas cell line with a precision of over 85%. To the best of our knowledge, this is the first time deep learning in the form of convolutional neural networks is applied to distinguish-with a high accuracy-apoptosis and necroptosis and alive cancer cells from each other in a label-free manner. It is expected that the approach described here will have a profound impact on research in regulated cell death, biomedicine and the field of (cancer) cell biology in general.
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Affiliation(s)
- Joost Verduijn
- grid.5342.00000 0001 2069 7798Nano-Biotechnology Laboratory, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium ,grid.510942.bCancer Research Institute Ghent, 9000 Ghent, Belgium
| | - Louis Van der Meeren
- grid.5342.00000 0001 2069 7798Nano-Biotechnology Laboratory, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium ,grid.510942.bCancer Research Institute Ghent, 9000 Ghent, Belgium
| | - Dmitri V. Krysko
- grid.510942.bCancer Research Institute Ghent, 9000 Ghent, Belgium ,grid.5342.00000 0001 2069 7798Cell Death Investigation and Therapy (CDIT) Laboratory, Anatomy an Embryology Unit, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium ,grid.448878.f0000 0001 2288 8774Department of Pathophysiology, Sechenov First Moscow State Medical University (Sechenov University), 119146 Moscow, Russian Federation
| | - André G. Skirtach
- grid.5342.00000 0001 2069 7798Nano-Biotechnology Laboratory, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium ,grid.510942.bCancer Research Institute Ghent, 9000 Ghent, Belgium
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35
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Manohar K, Gare S, Chel S, Dhyani V, Giri L. Quantitative Confocal Microscopy for Grouping of Dose-Response Data: Deciphering Calcium Sequestration and Subsequent Cell Death in the Presence of Excess Norepinephrine. SLAS Technol 2021; 26:454-467. [PMID: 34353144 DOI: 10.1177/24726303211019394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Fluorescent calcium (Ca2+) imaging is one of the preferred methods to record cellular activity during in vitro preclinical studies, high-content drug screening, and toxicity analysis. Visualization and analysis for dose-response data obtained using high-resolution imaging remain challenging, due to the inherent heterogeneity present in the Ca2+ spiking. To address this challenge, we propose measurement of cytosolic Ca2+ ions using spinning-disk confocal microscopy and machine learning-based analytics that is scalable. First, we implemented uniform manifold approximation and projection (UMAP) for visualizing the multivariate time-series dataset in the two-dimensional (2D) plane using Python. The dataset was obtained through live imaging experiments with norepinephrine-induced Ca2+ oscillation in HeLa cells for a large range of doses. Second, we demonstrate that the proposed framework can be used to depict the grouping of the spiking pattern for lower and higher drug doses. To the best of our knowledge, this is the first attempt at UMAP visualization of the time-series dose response and identification of the Ca2+ signature during lytic death. Such quantitative microscopy can be used as a component of a high-throughput data analysis workflow for toxicity analysis.
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Affiliation(s)
- Kuruba Manohar
- Department of BioTechnology, Indian Institute of Technology Hyderabad, Sangareddy, India
| | - Suman Gare
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Sangareddy, India
| | - Soumita Chel
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Sangareddy, India
| | - Vaibhav Dhyani
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Sangareddy, India
| | - Lopamudra Giri
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Sangareddy, India
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Beloglazova Y, Nikitiuk A, Voronina A, Gagarskikh O, Bayandin Y, Naimark O, Grishko V. Label-Free Single Cell Viability Assay Using Laser Interference Microscopy. BIOLOGY 2021; 10:590. [PMID: 34206974 PMCID: PMC8301067 DOI: 10.3390/biology10070590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 12/20/2022]
Abstract
Laser interference microscopy (LIM) is a promising label-free method for single-cell research applicable to cell viability assessment in the studies of mammalian cells. This paper describes the development of a sensitive and reproducible method for assessing cell viability using LIM. The method, based on associated signal processing techniques, has been developed as a result of real-time investigation in phase thickness fluctuations of viable and non-viable MCF-7 cells, reflecting the presence and absence of their metabolic activity. As evinced by the values of the variable vc, this variable determines the viability of a cell only in the attached state (vc exceeds 20 nm2 for viable attached cells). The critical value of the power spectrum slope βc of the phase thickness fluctuations equals 1.00 for attached MCF-7 cells and 0.71 for suspended cells. The slope of the phase fluctuations' power spectrum for MCF-7 cells was determined to exceed the threshold value of βc for a living cell, otherwise the cell is dead. The results evince the power spectrum slope as the most appropriate indicator of cell viability, while the integrated evaluation criterion (vc and βc values) can be used to assay the viability of attached cells.
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Affiliation(s)
- Yulia Beloglazova
- Perm Federal Scientific Centre, Institute of Technical Chemistry UB RAS, Academician Korolev St. 3, 614013 Perm, Russia; (Y.B.); (A.V.); (O.G.)
| | - Aleksandr Nikitiuk
- Perm Federal Scientific Centre, Institute of Continuous Media Mechanics UB RAS, Academician Korolev St. 1, 614013 Perm, Russia; (A.N.); (Y.B.); (O.N.)
| | - Anna Voronina
- Perm Federal Scientific Centre, Institute of Technical Chemistry UB RAS, Academician Korolev St. 3, 614013 Perm, Russia; (Y.B.); (A.V.); (O.G.)
| | - Olga Gagarskikh
- Perm Federal Scientific Centre, Institute of Technical Chemistry UB RAS, Academician Korolev St. 3, 614013 Perm, Russia; (Y.B.); (A.V.); (O.G.)
| | - Yuriy Bayandin
- Perm Federal Scientific Centre, Institute of Continuous Media Mechanics UB RAS, Academician Korolev St. 1, 614013 Perm, Russia; (A.N.); (Y.B.); (O.N.)
| | - Oleg Naimark
- Perm Federal Scientific Centre, Institute of Continuous Media Mechanics UB RAS, Academician Korolev St. 1, 614013 Perm, Russia; (A.N.); (Y.B.); (O.N.)
| | - Victoria Grishko
- Perm Federal Scientific Centre, Institute of Technical Chemistry UB RAS, Academician Korolev St. 3, 614013 Perm, Russia; (Y.B.); (A.V.); (O.G.)
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Qu HQ, Qu J, Dunn T, Snyder J, Miano TA, Connolly J, Glessner J, Anderson BJ, Reilly JP, Jones TK, Giannini HM, Agyekum RS, Weisman AR, Ittner CAG, Rodrigues LG, Kao C, Shashaty MGS, Sleiman P, Meyer NJ, Hakonarson H. Elevation of Circulating LIGHT (TNFSF14) and Interleukin-18 Levels in Sepsis-Induced Multi-Organ Injuries. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 34075388 DOI: 10.1101/2021.05.25.21257799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Objective The cytokines, LIGHT (TNFSF14) and Interleukin-18 (IL-18), are two important therapeutic targets due to their central roles in the function of activated T cells and inflammatory injury. LIGHT was recently shown to play a major role in COVID19 induced acute respiratory distress syndrome (ARDS), reducing mortality and hospital stay. This study aims to investigate the associations of LIGHT and IL-18 with non-COVID19 related ARDS, acute hypoxic respiratory failure (AHRF) or acute kidney injury (AKI), secondary to viral or bacterial sepsis. Research Design and Methods A cohort of 280 subjects diagnosed with sepsis, including 91 cases with sepsis triggered by viral infections, were investigated in this study and compared to healthy controls. Serum LIGHT, IL-18, and 59 other biomarkers (cytokines, chemokines and acute-phase reactants) were measured and associated with symptom severity. Results ARDS was observed in 36% of the patients, with 29% of the total patient cohort developing multi-organ failure (failure of two or more organs). We observed significantly increased LIGHT level (>2SD above mean of healthy subjects) in both bacterial sepsis patients (P=1.80E-05) and patients with sepsis from viral infections (P=1.78E-03). In bacterial sepsis, increased LIGHT level associated with ARDS, AKI and higher Apache III scores, findings also supported by correlations of LIGHT with other biomarkers of organ failures, suggesting LIGHT may be an inflammatory driver. IL-18 levels were highly variable across individuals, and consistently correlated with Apache III scores, mortality, and AKI, in both bacterial and viral sepsis. Conclusions For the first time, we demonstrate independent effects of LIGHT and IL-18 in septic organ failures. LIGHT levels are significantly elevated in non-COVID19 sepsis patients with ARDS and/or multi-organ failures suggesting that anti-LIGHT therapy may be effective therapy in a subset of patients with sepsis. Given the large variance of plasma IL-18 among septic subjects, targeting this pathway raises opportunities that require a precision application.
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You Z, Jiang M, Shi Z, Ning X, Shi C, Du S, Hérard AS, Jan C, Souedet N, Delzescaux T. Evaluation of automated segmentation algorithms for neurons in macaque cerebral microscopic images. Microsc Res Tech 2021; 84:2311-2324. [PMID: 33908123 DOI: 10.1002/jemt.23786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/21/2021] [Accepted: 04/07/2021] [Indexed: 11/12/2022]
Abstract
Accurate cerebral neuron segmentation is required before neuron counting and neuron morphological analysis. Numerous algorithms for neuron segmentation have been published, but they are mainly evaluated using limited subsets from a specific anatomical region, targeting neurons of clear contrast and/or neurons with similar staining intensity. It is thus unclear how these algorithms perform on cerebral neurons in diverse anatomical regions. In this article, we introduce and reliably evaluate existing machine learning algorithms using a data set of microscopy images of macaque brain. This data set highlights various anatomical regions (e.g., cortex, caudate, thalamus, claustrum, putamen, hippocampus, subiculum, lateral geniculate, globus pallidus, etc.), poor contrast, and staining intensity differences of neurons. The evaluation was performed using 10 architectures of six classic machine learning algorithms in terms of typical Recall, Precision, F-score, aggregated Jaccard index (AJI), as well as a performance ranking of algorithms. F-score of most of the algorithms is superior to 0.7. Deep learning algorithms facilitate generally higher F-scores. U-net with suitable layer depth has been evaluated to be excellent classifiers with F-score of 0.846 and 0.837 when performing cross validation. The evaluation and analysis indicate the performance gap among algorithms in various anatomical regions and the strengths and limitations of each algorithm. The comparative result highlights at the same time the importance and difficulty of neuron segmentation and provides clues for future improvement. To the best of our knowledge, this work is the first comprehensive study for neuron segmentation in such large-scale anatomical regions.
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Affiliation(s)
- Zhenzhen You
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, China.,CEA-CNRS-UMR 9199, Laboratoire des Maladies Neurodégénératives, MIRCen, Fontenay-aux-Roses, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Ming Jiang
- National Laboratory of Radar Signal Processing, Xidian University, Xi'an, China
| | - Zhenghao Shi
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, China
| | - Xiaojuan Ning
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, China
| | - Cheng Shi
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, China
| | - Shuangli Du
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, China
| | - Anne-Sophie Hérard
- CEA-CNRS-UMR 9199, Laboratoire des Maladies Neurodégénératives, MIRCen, Fontenay-aux-Roses, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Caroline Jan
- CEA-CNRS-UMR 9199, Laboratoire des Maladies Neurodégénératives, MIRCen, Fontenay-aux-Roses, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Nicolas Souedet
- CEA-CNRS-UMR 9199, Laboratoire des Maladies Neurodégénératives, MIRCen, Fontenay-aux-Roses, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Thierry Delzescaux
- CEA-CNRS-UMR 9199, Laboratoire des Maladies Neurodégénératives, MIRCen, Fontenay-aux-Roses, Université Paris-Saclay, Gif-sur-Yvette, France
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Broad-Spectrum Antiviral Activity of 3'-Deoxy-3'-Fluoroadenosine against Emerging Flaviviruses. Antimicrob Agents Chemother 2021; 65:AAC.01522-20. [PMID: 33229424 DOI: 10.1128/aac.01522-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/14/2020] [Indexed: 01/23/2023] Open
Abstract
Emerging flaviviruses are causative agents of severe and life-threatening diseases, against which no approved therapies are available. Among the nucleoside analogues, which represent a promising group of potentially therapeutic compounds, fluorine-substituted nucleosides are characterized by unique structural and functional properties. Despite having first been synthesized almost 5 decades ago, they still offer new therapeutic opportunities as inhibitors of essential viral or cellular enzymes active in nucleic acid replication/transcription or nucleoside/nucleotide metabolism. Here, we report evaluation of the antiflaviviral activity of 28 nucleoside analogues, each modified with a fluoro substituent at different positions of the ribose ring and/or heterocyclic nucleobase. Our antiviral screening revealed that 3'-deoxy-3'-fluoroadenosine exerted a low-micromolar antiviral effect against tick-borne encephalitis virus (TBEV), Zika virus, and West Nile virus (WNV) (EC50 values from 1.1 ± 0.1 μM to 4.7 ± 1.5 μM), which was manifested in host cell lines of neural and extraneural origin. The compound did not display any measurable cytotoxicity up to concentrations of 25 μM but had an observable cytostatic effect, resulting in suppression of cell proliferation at concentrations of >12.5 μM. Novel approaches based on quantitative phase imaging using holographic microscopy were developed for advanced characterization of antiviral and cytotoxic profiles of 3'-deoxy-3'-fluoroadenosine in vitro In addition to its antiviral activity in cell cultures, 3'-deoxy-3'-fluoroadenosine was active in vivo in mouse models of TBEV and WNV infection. Our results demonstrate that fluoro-modified nucleosides represent a group of bioactive molecules with excellent potential to serve as prospective broad-spectrum antivirals in antiviral research and drug development.
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Indianto MA, Toda M, Ono T. Development of assembled microchannel resonator as an alternative fabrication method of a microchannel resonator for mass sensing in flowing liquid. BIOMICROFLUIDICS 2020; 14:064111. [PMID: 33381251 PMCID: PMC7748827 DOI: 10.1063/5.0032040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
We propose an alternate fabrication technique of microchannel resonators based on an assembly method of three separate parts to form a microchannel resonator on a chip. The capability of the assembled microchannel resonator to detect mass is confirmed by injecting two liquids with different densities. The experimental and theoretical values of the resonator frequency shift are in agreement with each other, which confirms the consistency of the device. The noise level of the device is estimated from the Allan variance plot, so the minimum detectable mass of 230 fg after 16 s of operation is expected. By considering the time of the practical application of 1 ms, it is found that a detectable mass of around 8.51 pg is estimated, which is applicable for detecting flowing microparticles. The sub-pico to a few picogram levels of detection will be applicable for the mass analysis of flowing microparticles such as single cells and will be greatly beneficial for many fields such as chemistry, medicine, biology, and single-cell analysis.
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O’Connor T, Anand A, Andemariam B, Javidi B. Deep learning-based cell identification and disease diagnosis using spatio-temporal cellular dynamics in compact digital holographic microscopy. BIOMEDICAL OPTICS EXPRESS 2020; 11:4491-4508. [PMID: 32923059 PMCID: PMC7449709 DOI: 10.1364/boe.399020] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/01/2020] [Accepted: 07/12/2020] [Indexed: 05/14/2023]
Abstract
We demonstrate a successful deep learning strategy for cell identification and disease diagnosis using spatio-temporal cell information recorded by a digital holographic microscopy system. Shearing digital holographic microscopy is employed using a low-cost, compact, field-portable and 3D-printed microscopy system to record video-rate data of live biological cells with nanometer sensitivity in terms of axial membrane fluctuations, then features are extracted from the reconstructed phase profiles of segmented cells at each time instance for classification. The time-varying data of each extracted feature is input into a recurrent bi-directional long short-term memory (Bi-LSTM) network which learns to classify cells based on their time-varying behavior. Our approach is presented for cell identification between the morphologically similar cases of cow and horse red blood cells. Furthermore, the proposed deep learning strategy is demonstrated as having improved performance over conventional machine learning approaches on a clinically relevant dataset of human red blood cells from healthy individuals and those with sickle cell disease. The results are presented at both the cell and patient levels. To the best of our knowledge, this is the first report of deep learning for spatio-temporal-based cell identification and disease detection using a digital holographic microscopy system.
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Affiliation(s)
- Timothy O’Connor
- Biomedical Engineering Department, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Arun Anand
- Applied Physics Department, Faculty of Tech. & Engineering, M.S. University of Baroda, Vadodara 390001, India
| | - Biree Andemariam
- New England Sickle Cell Institute, University of Connecticut Health, Farmington, Connecticut 06030, USA
| | - Bahram Javidi
- Electrical and Computer Engineering Department, University of Connecticut, Storrs, Connecticut 06269, USA
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Quantitative Phase Dynamics of Cancer Cell Populations Affected by Blue Light. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10072597] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Increased exposition to blue light may induce many changes in cell behavior and significantly affect the critical characteristics of cells. Here we show that multimodal holographic microscopy (MHM) within advanced image analysis is capable of correctly distinguishing between changes in cell motility, cell dry mass, cell density, and cell death induced by blue light. We focused on the effect of blue light with a wavelength of 485 nm on morphological and dynamical parameters of four cell lines, malignant PC-3, A2780, G361 cell lines, and the benign PNT1A cell line. We used MHM with blue light doses 24 mJ/cm2, 208 mJ/cm2 and two kinds of expositions (500 and 1000 ms) to acquire real-time quantitative phase information about cellular parameters. It has been shown that specific doses of the blue light significantly influence cell motility, cell dry mass and cell density. These changes were often specific for the malignant status of tested cells. Blue light dose 208 mJ/cm2 × 1000 ms affected malignant cell motility but did not change the motility of benign cell line PNT1A. This light dose also significantly decreased proliferation activity in all tested cell lines but was not so deleterious for benign cell line PNT1A as for malignant cells. Light dose 208 mJ/cm2 × 1000 ms oppositely affected cell mass in A2780 and PC-3 cells and induced different types of cell death in A2780 and G361 cell lines. Cells obtained the least damage on lower doses of light with shorter time of exposition.
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