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Sbrana F, Chellini F, Tani A, Parigi M, Garella R, Palmieri F, Zecchi-Orlandini S, Squecco R, Sassoli C. Label-free three-dimensional imaging and quantitative analysis of living fibroblasts and myofibroblasts by holotomographic microscopy. Microsc Res Tech 2024; 87:2757-2773. [PMID: 38984377 DOI: 10.1002/jemt.24648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/11/2024]
Abstract
Holotomography (HT) is a cutting-edge fast live-cell quantitative label-free imaging technique. Based on the principle of quantitative phase imaging, it combines holography and tomography to record a three-dimensional map of the refractive index, used as intrinsic optical and quantitative imaging contrast parameter of biological samples, at a sub-micrometer spatial resolution. In this study HT has been employed for the first time to analyze the changes of fibroblasts differentiating towards myofibroblasts - recognized as the main cell player of fibrosis - when cultured in vitro with the pro-fibrotic factor, namely transforming growth factor-β1. In parallel, F-actin, vinculin, α-smooth muscle actin, phospho-myosin light chain 2, type-1 collagen, peroxisome proliferator-activated receptor-gamma coactivator-1α expression and mitochondria were evaluated by confocal laser scanning microscopy. Plasmamembrane passive properties and transient receptor potential canonical channels' currents were also recorded by whole-cell patch-clamp. The fluorescence images and electrophysiological results have been compared to the data obtained by HT and their congruence has been discussed. HT turned out to be a valid approach to morphologically distinguish fibroblasts from well differentiated myofibroblasts while obtaining objective measures concerning volume, surface area, projection area, surface index and dry mass (i.e., the mass of the non-aqueous content inside the cell including proteins and subcellular organelles) of the entire cell, nuclei and nucleoli with the major advantage to monitor outer and inner features in living cells in a non-invasive, rapid and label-free approach. HT might open up new research opportunities in the field of fibrotic diseases. RESEARCH HIGHLIGHTS: Holotomography (HT) is a label-free laser interferometric imaging technology exploiting the intrinsic optical property of cells namely refractive index (RI) to enable a direct imaging and analysis of whole cells or intracellular organelles. HT turned out a valid approach to distinguish morphological features of living unlabeled fibroblasts from differentiated myofibroblasts. HT provided quantitative information concerning volume, surface area, projection area, surface index and dry mass of the entire fibroblasts/myofibroblasts, nuclei and nucleoli.
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Affiliation(s)
| | - Flaminia Chellini
- Department of Experimental and Clinical Medicine, Section of Anatomy and Histology, Imaging Platform, University of Florence, Florence, Italy
| | - Alessia Tani
- Department of Experimental and Clinical Medicine, Section of Anatomy and Histology, Imaging Platform, University of Florence, Florence, Italy
| | - Martina Parigi
- Department of Experimental and Clinical Medicine, Section of Anatomy and Histology, Imaging Platform, University of Florence, Florence, Italy
| | - Rachele Garella
- Department of Experimental and Clinical Medicine, Section of Physiological Sciences, University of Florence, Florence, Italy
| | - Francesco Palmieri
- Department of Experimental and Clinical Medicine, Section of Physiological Sciences, University of Florence, Florence, Italy
| | - Sandra Zecchi-Orlandini
- Department of Experimental and Clinical Medicine, Section of Anatomy and Histology, Imaging Platform, University of Florence, Florence, Italy
| | - Roberta Squecco
- Department of Experimental and Clinical Medicine, Section of Physiological Sciences, University of Florence, Florence, Italy
| | - Chiara Sassoli
- Department of Experimental and Clinical Medicine, Section of Anatomy and Histology, Imaging Platform, University of Florence, Florence, Italy
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2
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Wang Z, Wang J, Zhao Y, Jin J, Si W, Chen L, Zhang M, Zhou Y, Mao S, Zheng C, Zhang Y, Chen L, Fei P. 3D live imaging and phenotyping of CAR-T cell mediated-cytotoxicity using high-throughput Bessel oblique plane microscopy. Nat Commun 2024; 15:6677. [PMID: 39107283 PMCID: PMC11303822 DOI: 10.1038/s41467-024-51039-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 07/29/2024] [Indexed: 08/10/2024] Open
Abstract
Clarification of the cytotoxic function of T cells is crucial for understanding human immune responses and immunotherapy procedures. Here, we report a high-throughput Bessel oblique plane microscopy (HBOPM) platform capable of 3D live imaging and phenotyping of chimeric antigen receptor (CAR)-modified T-cell cytotoxicity against cancer cells. The HBOPM platform has the following characteristics: an isotropic subcellular resolution of 320 nm, large-scale scouting over 400 interacting cell pairs, long-term observation across 5 hours, and quantitative analysis of the Terabyte-scale 3D, multichannel, time-lapse image datasets. Using this advanced microscopy platform, several key subcellular events in CAR-T cells are captured and comprehensively analyzed; these events include the instantaneous formation of immune synapses and the sustained changes in the microtubing morphology. Furthermore, we identify the actin retrograde flow speed, the actin depletion coefficient, the microtubule polarization and the contact area of the CAR-T/target cell conjugates as essential parameters strongly correlated with CAR-T-cell cytotoxic function. Our approach will be useful for establishing criteria for quantifying T-cell function in individual patients for all T-cell-based immunotherapies.
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Affiliation(s)
- Zhaofei Wang
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jie Wang
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yuxuan Zhao
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jin Jin
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wentian Si
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Longbiao Chen
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Man Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yao Zhou
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Shiqi Mao
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Chunhong Zheng
- International Cancer Institute, Peking University Cancer Hospital and Institute, Peking University, Beijing, China
| | - Yicheng Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liting Chen
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Peng Fei
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
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3
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Elmalam N, Ben Nedava L, Zaritsky A. In silico labeling in cell biology: Potential and limitations. Curr Opin Cell Biol 2024; 89:102378. [PMID: 38838549 DOI: 10.1016/j.ceb.2024.102378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 06/07/2024]
Abstract
In silico labeling is the computational cross-modality image translation where the output modality is a subcellular marker that is not specifically encoded in the input image, for example, in silico localization of organelles from transmitted light images. In principle, in silico labeling has the potential to facilitate rapid live imaging of multiple organelles with reduced photobleaching and phototoxicity, a technology enabling a major leap toward understanding the cell as an integrated complex system. However, five years have passed since feasibility was attained, without any demonstration of using in silico labeling to uncover new biological insight. In here, we discuss the current state of in silico labeling, the limitations preventing it from becoming a practical tool, and how we can overcome these limitations to reach its full potential.
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Affiliation(s)
- Nitsan Elmalam
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Lion Ben Nedava
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Assaf Zaritsky
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
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Kim SE, Yun S, Doh J, Kim HN. Imaging-Based Efficacy Evaluation of Cancer Immunotherapy in Engineered Tumor Platforms and Tumor Organoids. Adv Healthc Mater 2024:e2400475. [PMID: 38815251 DOI: 10.1002/adhm.202400475] [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: 02/06/2024] [Revised: 05/16/2024] [Indexed: 06/01/2024]
Abstract
Cancer immunotherapy is used to treat tumors by modulating the immune system. Although the anticancer efficacy of cancer immunotherapy has been evaluated prior to clinical trials, conventional in vivo animal and endpoint models inadequately replicate the intricate process of tumor elimination and reflect human-specific immune systems. Therefore, more sophisticated models that mimic the complex tumor-immune microenvironment must be employed to assess the effectiveness of immunotherapy. Additionally, using real-time imaging technology, a step-by-step evaluation can be applied, allowing for a more precise assessment of treatment efficacy. Here, an overview of the various imaging-based evaluation platforms recently developed for cancer immunotherapeutic applications is presented. Specifically, a fundamental technique is discussed for stably observing immune cell-based tumor cell killing using direct imaging, a microwell that reproduces a confined space for spatial observation, a droplet assay that facilitates cell-cell interactions, and a 3D microphysiological system that reconstructs the vascular environment. Furthermore, it is suggested that future evaluation platforms pursue more human-like immune systems.
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Affiliation(s)
- Seong-Eun Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea
| | - Suji Yun
- Interdisciplinary Program for Bioengineering, Seoul National University, Seoul, 08826, South Korea
| | - Junsang Doh
- Interdisciplinary Program for Bioengineering, Seoul National University, Seoul, 08826, South Korea
- Department of Materials Science and Engineering, Research Institute of Advanced Materials, Institute of Engineering Research, Bio-MAX institute, Soft Foundry Institute, Seoul National University, Seoul, 08826, South Korea
| | - Hong Nam Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, Republic of Korea
- School of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea
- Yonsei-KIST Convergence Research Institute, Yonsei University, Seoul, 03722, Republic of Korea
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5
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Martín-Antonio B, Blanco B, González-Murillo Á, Hidalgo L, Minguillón J, Pérez-Chacón G. Newer generations of multi-target CAR and STAb-T immunotherapeutics: NEXT CART Consortium as a cooperative effort to overcome current limitations. Front Immunol 2024; 15:1386856. [PMID: 38779672 PMCID: PMC11109416 DOI: 10.3389/fimmu.2024.1386856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Adoptive T cellular immunotherapies have emerged as relevant approaches for treating cancer patients who have relapsed or become refractory (R/R) to traditional cancer treatments. Chimeric antigen receptor (CAR) T-cell therapy has improved survival in various hematological malignancies. However, significant limitations still impede the widespread adoption of these therapies in most cancers. To advance in this field, six research groups have created the "NEXT Generation CART MAD Consortium" (NEXT CART) in Madrid's Community, which aims to develop novel cell-based immunotherapies for R/R and poor prognosis cancers. At NEXT CART, various basic and translational research groups and hospitals in Madrid concur to share and synergize their basic expertise in immunotherapy, gene therapy, and immunological synapse, and clinical expertise in pediatric and adult oncology. NEXT CART goal is to develop new cell engineering approaches and treatments for R/R adult and pediatric neoplasms to evaluate in multicenter clinical trials. Here, we discuss the current limitations of T cell-based therapies and introduce our perspective on future developments. Advancement opportunities include developing allogeneic products, optimizing CAR signaling domains, combining cellular immunotherapies, multi-targeting strategies, and improving tumor-infiltrating lymphocytes (TILs)/T cell receptor (TCR) therapy. Furthermore, basic studies aim to identify novel tumor targets, tumor molecules in the tumor microenvironment that impact CAR efficacy, and strategies to enhance the efficiency of the immunological synapse between immune and tumor cells. Our perspective of current cellular immunotherapy underscores the potential of these treatments while acknowledging the existing hurdles that demand innovative solutions to develop their potential for cancer treatment fully.
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Affiliation(s)
- Beatriz Martín-Antonio
- Department of Experimental Hematology, Instituto de Investigación Sanitaria-Fundación Jiménez Diaz (IIS-FJD), Madrid, Spain
| | - Belén Blanco
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
| | - África González-Murillo
- Department of Pediatric Hematology and Oncology, Advanced Therapies Unit, Fundación Investigación Biomédica Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Laura Hidalgo
- Cellular Biotechnology Unit, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Jordi Minguillón
- La Paz Hospital Institute for Health Research (IdiPAZ), Hospital Universitario La Paz. Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Gema Pérez-Chacón
- Immunity, Immunopathology and Emergent Therapies Group. Instituto de Investigaciones Biomedicas Sols-Morreale. CSIC-UAM, Madrid, Spain
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Lee M, Jeong H, Lee C, Lee MJ, Delmo BR, Heo WD, Shin JH, Park Y. High-resolution assessment of multidimensional cellular mechanics using label-free refractive-index traction force microscopy. Commun Biol 2024; 7:115. [PMID: 38245624 PMCID: PMC10799850 DOI: 10.1038/s42003-024-05788-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 01/03/2024] [Indexed: 01/22/2024] Open
Abstract
A critical requirement for studying cell mechanics is three-dimensional assessment of cellular shapes and forces with high spatiotemporal resolution. Traction force microscopy with fluorescence imaging enables the measurement of cellular forces, but it is limited by photobleaching and a slow acquisition speed. Here, we present refractive-index traction force microscopy (RI-TFM), which simultaneously quantifies the volumetric morphology and traction force of cells using a high-speed illumination scheme with 0.5-Hz temporal resolution. Without labelling, our method enables quantitative analyses of dry-mass distributions and shear (in-plane) and normal (out-of-plane) tractions of single cells on the extracellular matrix. When combined with a constrained total variation-based deconvolution algorithm, it provides 0.55-Pa shear and 1.59-Pa normal traction sensitivity for a 1-kPa hydrogel substrate. We demonstrate its utility by assessing the effects of compromised intracellular stress and capturing the rapid dynamics of cellular junction formation in the spatiotemporal changes in non-planar traction components.
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Affiliation(s)
- Moosung Lee
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, South Korea
- Institute for Functional Matter and Quantum Technologies, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Hyuntae Jeong
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Chaeyeon Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Mahn Jae Lee
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, South Korea
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Benedict Reve Delmo
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Won Do Heo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea.
- KAIST Institute for the BioCentury (KIB), KAIST, Jaejeo, Daejeon, 34141, South Korea.
| | - Jennifer H Shin
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea.
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea.
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, South Korea.
- Tomocube Inc., Daejeon, 34109, South Korea.
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7
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Lee MJ, Kim B, Lee D, Kim G, Chung Y, Shin HS, Choi S, Park Y. Enhanced functionalities of immune cells separated by a microfluidic lattice: assessment based on holotomography. BIOMEDICAL OPTICS EXPRESS 2023; 14:6127-6137. [PMID: 38420329 PMCID: PMC10898572 DOI: 10.1364/boe.503957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 03/02/2024]
Abstract
The isolation of white blood cells (WBCs) from whole blood constitutes a pivotal process for immunological studies, diagnosis of hematologic disorders, and the facilitation of immunotherapy. Despite the ubiquity of density gradient centrifugation in WBC isolation, its influence on WBC functionality remains inadequately understood. This research employs holotomography to explore the effects of two distinct WBC separation techniques, namely conventional centrifugation and microfluidic separation, on the functionality of the isolated cells. We utilize three-dimensional refractive index distribution and time-lapse dynamics to analyze individual WBCs in-depth, focusing on their morphology, motility, and phagocytic capabilities. Our observations highlight that centrifugal processes negatively impact WBC motility and phagocytic capacity, whereas microfluidic separation yields a more favorable outcome in preserving WBC functionality. These findings emphasize the potential of microfluidic separation techniques as a viable alternative to traditional centrifugation for WBC isolation, potentially enabling more precise analyses in immunology research and improving the accuracy of hematologic disorder diagnoses.
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Affiliation(s)
- Mahn Jae Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Byungyeon Kim
- Department of Electronic Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Dohyeon Lee
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Department of Physics, KAIST, Daejeon 34141, Republic of Korea
| | - Geon Kim
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Department of Physics, KAIST, Daejeon 34141, Republic of Korea
| | - Yoonjae Chung
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Department of Physics, KAIST, Daejeon 34141, Republic of Korea
| | - Hee Sik Shin
- Department of Electronic Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Sungyoung Choi
- Department of Electronic Engineering, Hanyang University, Seoul 04763, Republic of Korea
- Department of Biomedical Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - YongKeun Park
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Department of Electronic Engineering, Hanyang University, Seoul 04763, Republic of Korea
- Tomocube Inc., Daejeon 34109, Republic of Korea
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Park J, Bai B, Ryu D, Liu T, Lee C, Luo Y, Lee MJ, Huang L, Shin J, Zhang Y, Ryu D, Li Y, Kim G, Min HS, Ozcan A, Park Y. Artificial intelligence-enabled quantitative phase imaging methods for life sciences. Nat Methods 2023; 20:1645-1660. [PMID: 37872244 DOI: 10.1038/s41592-023-02041-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 09/11/2023] [Indexed: 10/25/2023]
Abstract
Quantitative phase imaging, integrated with artificial intelligence, allows for the rapid and label-free investigation of the physiology and pathology of biological systems. This review presents the principles of various two-dimensional and three-dimensional label-free phase imaging techniques that exploit refractive index as an intrinsic optical imaging contrast. In particular, we discuss artificial intelligence-based analysis methodologies for biomedical studies including image enhancement, segmentation of cellular or subcellular structures, classification of types of biological samples and image translation to furnish subcellular and histochemical information from label-free phase images. We also discuss the advantages and challenges of artificial intelligence-enabled quantitative phase imaging analyses, summarize recent notable applications in the life sciences, and cover the potential of this field for basic and industrial research in the life sciences.
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Affiliation(s)
- Juyeon Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea
| | - Bijie Bai
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA
- Bioengineering Department, University of California, Los Angeles, Los Angeles, CA, USA
| | - DongHun Ryu
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tairan Liu
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA
| | - Chungha Lee
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea
| | - Yi Luo
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mahn Jae Lee
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Luzhe Huang
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jeongwon Shin
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Yijie Zhang
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Yuzhu Li
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA
| | - Geon Kim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea
| | | | - Aydogan Ozcan
- Electrical and Computer Engineering Department, University of California, Los Angeles, Los Angeles, CA, USA.
- Bioengineering Department, University of California, Los Angeles, Los Angeles, CA, USA.
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, Republic of Korea.
- Tomocube, Daejeon, Republic of Korea.
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Wu KL, Martinez-Paniagua M, Reichel K, Menon PS, Deo S, Roysam B, Varadarajan N. Automated detection of apoptotic bodies and cells in label-free time-lapse high-throughput video microscopy using deep convolutional neural networks. Bioinformatics 2023; 39:btad584. [PMID: 37773981 PMCID: PMC10563152 DOI: 10.1093/bioinformatics/btad584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 09/06/2023] [Accepted: 09/28/2023] [Indexed: 10/01/2023] Open
Abstract
MOTIVATION Reliable label-free methods are needed for detecting and profiling apoptotic events in time-lapse cell-cell interaction assays. Prior studies relied on fluorescent markers of apoptosis, e.g. Annexin-V, that provide an inconsistent and late indication of apoptotic onset for human melanoma cells. Our motivation is to improve the detection of apoptosis by directly detecting apoptotic bodies in a label-free manner. RESULTS Our trained ResNet50 network identified nanowells containing apoptotic bodies with 92% accuracy and predicted the onset of apoptosis with an error of one frame (5 min/frame). Our apoptotic body segmentation yielded an IoU accuracy of 75%, allowing associative identification of apoptotic cells. Our method detected apoptosis events, 70% of which were not detected by Annexin-V staining. AVAILABILITY AND IMPLEMENTATION Open-source code and sample data provided at https://github.com/kwu14victor/ApoBDproject.
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Affiliation(s)
- Kwan-Ling Wu
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, United States
| | - Melisa Martinez-Paniagua
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, United States
| | - Kate Reichel
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, United States
| | - Prashant S Menon
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, United States
| | - Shravani Deo
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, United States
| | - Badrinath Roysam
- Department of Electrical and Computer Engineering, University of Houston, Houston, TX 77204, United States
| | - Navin Varadarajan
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, United States
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10
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Mazur M, Krauze W. Volumetric segmentation of biological cells and subcellular structures for optical diffraction tomography images. BIOMEDICAL OPTICS EXPRESS 2023; 14:5022-5035. [PMID: 37854559 PMCID: PMC10581803 DOI: 10.1364/boe.498275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 10/20/2023]
Abstract
Three-dimensional, quantitative imaging of biological cells and their internal structures performed by optical diffraction tomography (ODT) is an important part of biomedical research. However, conducting quantitative analysis of ODT images requires performing 3D segmentation with high accuracy, often unattainable with available segmentation methods. Therefore, in this work, we present a new semi-automatic method, called ODT-SAS, which combines several non-machine-learning techniques to segment cells and 2 types of their organelles: nucleoli and lipid structures (LS). ODT-SAS has been compared with Cellpose and slice-by-slice manual segmentation, respectively, in cell segmentation and organelles segmentation. The comparison shows superiority of ODT-SAS over Cellpose and reveals the potential of our technique in detecting cells, nucleoli and LS.
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Affiliation(s)
- Martyna Mazur
- Warsaw University of Technology, 8 Boboli Str., Warsaw, 02-525, Poland
| | - Wojciech Krauze
- Warsaw University of Technology, 8 Boboli Str., Warsaw, 02-525, Poland
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11
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Bäckel N, Hort S, Kis T, Nettleton DF, Egan JR, Jacobs JJL, Grunert D, Schmitt RH. Elaborating the potential of Artificial Intelligence in automated CAR-T cell manufacturing. FRONTIERS IN MOLECULAR MEDICINE 2023; 3:1250508. [PMID: 39086671 PMCID: PMC11285580 DOI: 10.3389/fmmed.2023.1250508] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 08/28/2023] [Indexed: 08/02/2024]
Abstract
This paper discusses the challenges of producing CAR-T cells for cancer treatment and the potential for Artificial Intelligence (AI) for its improvement. CAR-T cell therapy was approved in 2018 as the first Advanced Therapy Medicinal Product (ATMP) for treating acute leukemia and lymphoma. ATMPs are cell- and gene-based therapies that show great promise for treating various cancers and hereditary diseases. While some new ATMPs have been approved, ongoing clinical trials are expected to lead to the approval of many more. However, the production of CAR-T cells presents a significant challenge due to the high costs associated with the manufacturing process, making the therapy very expensive (approx. $400,000). Furthermore, autologous CAR-T therapy is limited to a make-to-order approach, which makes scaling economical production difficult. First attempts are being made to automate this multi-step manufacturing process, which will not only directly reduce the high manufacturing costs but will also enable comprehensive data collection. AI technologies have the ability to analyze this data and convert it into knowledge and insights. In order to exploit these opportunities, this paper analyses the data potential in the automated CAR-T production process and creates a mapping to the capabilities of AI applications. The paper explores the possible use of AI in analyzing the data generated during the automated process and its capabilities to further improve the efficiency and cost-effectiveness of CAR-T cell production.
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Affiliation(s)
- Niklas Bäckel
- Fraunhofer Institute for Production Technology IPT, Aachen, Germany
| | - Simon Hort
- Fraunhofer Institute for Production Technology IPT, Aachen, Germany
| | - Tamás Kis
- Institute for Computer Science and Control, Hungarian Research Network, Budapest, Hungary
| | | | - Joseph R. Egan
- Department of Biochemical Engineering, Mathematical Modelling of Cell and Gene Therapies, University College London, London, United Kingdom
| | | | - Dennis Grunert
- Fraunhofer Institute for Production Technology IPT, Aachen, Germany
| | - Robert H. Schmitt
- Fraunhofer Institute for Production Technology IPT, Aachen, Germany
- Laboratory for Machine Tools and Production Engineering (WZL), RWTH Aachen University, Aachen, Germany
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12
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Lee M, Kunzi M, Neurohr G, Lee SS, Park Y. Hybrid machine-learning framework for volumetric segmentation and quantification of vacuoles in individual yeast cells using holotomography. BIOMEDICAL OPTICS EXPRESS 2023; 14:4567-4578. [PMID: 37791265 PMCID: PMC10545186 DOI: 10.1364/boe.498475] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/23/2023] [Accepted: 07/31/2023] [Indexed: 10/05/2023]
Abstract
The precise, quantitative evaluation of intracellular organelles in three-dimensional (3D) imaging data poses a significant challenge due to the inherent constraints of traditional microscopy techniques, the requirements of the use of exogenous labeling agents, and existing computational methods. To counter these challenges, we present a hybrid machine-learning framework exploiting correlative imaging of 3D quantitative phase imaging with 3D fluorescence imaging of labeled cells. The algorithm, which synergistically integrates a random-forest classifier with a deep neural network, is trained using the correlative imaging data set, and the trained network is then applied to 3D quantitative phase imaging of cell data. We applied this method to live budding yeast cells. The results revealed precise segmentation of vacuoles inside individual yeast cells, and also provided quantitative evaluations of biophysical parameters, including volumes, concentration, and dry masses of automatically segmented vacuoles.
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Affiliation(s)
- Moosung Lee
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Current affiliation: Institute for Functional Matter and Quantum Technologies, Universität Stuttgart, 70569 Stuttgart, Germany
| | - Marina Kunzi
- Institute for Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
- Bringing Materials to Life Initiative, ETH Zürich, Zürich, Switzerland
| | - Gabriel Neurohr
- Institute for Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
- Bringing Materials to Life Initiative, ETH Zürich, Zürich, Switzerland
| | - Sung Sik Lee
- Institute for Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
- Bringing Materials to Life Initiative, ETH Zürich, Zürich, Switzerland
- ScopeM (Scientific Center of Optical and Electron Microscopy), ETH Zürich, 8093, Zurich, Switzerland
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Tomocube Inc., Daejeon 34051, Republic of Korea
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13
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Kang S, Zhou R, Brelen M, Mak HK, Lin Y, So PTC, Yaqoob Z. Mapping nanoscale topographic features in thick tissues with speckle diffraction tomography. LIGHT, SCIENCE & APPLICATIONS 2023; 12:200. [PMID: 37607903 PMCID: PMC10444882 DOI: 10.1038/s41377-023-01240-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/11/2023] [Accepted: 07/19/2023] [Indexed: 08/24/2023]
Abstract
Resolving three-dimensional morphological features in thick specimens remains a significant challenge for label-free imaging. We report a new speckle diffraction tomography (SDT) approach that can image thick biological specimens with ~500 nm lateral resolution and ~1 μm axial resolution in a reflection geometry. In SDT, multiple-scattering background is rejected through spatiotemporal gating provided by dynamic speckle-field interferometry, while depth-resolved refractive index maps are reconstructed by developing a comprehensive inverse-scattering model that also considers specimen-induced aberrations. Benefiting from the high-resolution and full-field quantitative imaging capabilities of SDT, we successfully imaged red blood cells and quantified their membrane fluctuations behind a turbid medium with a thickness of 2.8 scattering mean-free paths. Most importantly, we performed volumetric imaging of cornea inside an ex vivo rat eye and quantified its optical properties, including the mapping of nanoscale topographic features of Dua's and Descemet's membranes that had not been previously visualized.
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Affiliation(s)
- Sungsam Kang
- Laser Biomedical Research Center, G. R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Renjie Zhou
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China.
| | - Marten Brelen
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Heather K Mak
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuechuan Lin
- Laser Biomedical Research Center, G. R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Peter T C So
- Laser Biomedical Research Center, G. R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Zahid Yaqoob
- Laser Biomedical Research Center, G. R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
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14
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Ryu D, Bak T, Ahn D, Kang H, Oh S, Min HS, Lee S, Lee J. Deep learning-based label-free hematology analysis framework using optical diffraction tomography. Heliyon 2023; 9:e18297. [PMID: 37576294 PMCID: PMC10412892 DOI: 10.1016/j.heliyon.2023.e18297] [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: 03/04/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 08/15/2023] Open
Abstract
Hematology analysis, a common clinical test for screening various diseases, has conventionally required a chemical staining process that is time-consuming and labor-intensive. To reduce the costs of chemical staining, label-free imaging can be utilized in hematology analysis. In this work, we exploit optical diffraction tomography and the fully convolutional one-stage object detector or FCOS, a deep learning architecture for object detection, to develop a label-free hematology analysis framework. Detected cells are classified into four groups: red blood cell, abnormal red blood cell, platelet, and white blood cell. In the results, the trained object detection model showed superior detection performance for blood cells in refractive index tomograms (0.977 mAP) and also showed high accuracy in the four-class classification of blood cells (0.9708 weighted F1 score, 0.9712 total accuracy). For further verification, mean corpuscular volume (MCV) and mean corpuscular hemoglobin (MCH) were compared with values obtained from reference hematology equipment, with our results showing reasonable correlation in both MCV (0.905) and MCH (0.889). This study provides a successful demonstration of the proposed framework in detecting and classifying blood cells using optical diffraction tomography for label-free hematology analysis.
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Affiliation(s)
- Dongmin Ryu
- Tomocube Inc., Daejeon, 34109, Republic of Korea
| | - Taeyoung Bak
- Department of Computer Science and Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Daewoong Ahn
- Tomocube Inc., Daejeon, 34109, Republic of Korea
| | - Hayoung Kang
- Tomocube Inc., Daejeon, 34109, Republic of Korea
| | - Sanggeun Oh
- Tomocube Inc., Daejeon, 34109, Republic of Korea
| | | | - Sumin Lee
- Tomocube Inc., Daejeon, 34109, Republic of Korea
| | - Jimin Lee
- Department of Nuclear Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- Graduate School of Artificial Intelligence (AIGS), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
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15
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Tanwar S, Wu L, Zahn N, Raj P, Ghaemi B, Chatterjee A, Bulte JWM, Barman I. Targeted Enzyme Activity Imaging with Quantitative Phase Microscopy. NANO LETTERS 2023; 23:4602-4608. [PMID: 37154678 PMCID: PMC10798004 DOI: 10.1021/acs.nanolett.3c01090] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Quantitative phase imaging (QPI) is a powerful optical imaging modality for label-free, rapid, and three-dimensional (3D) monitoring of cells and tissues. However, molecular imaging of important intracellular biomolecules such as enzymes remains a largely unexplored area for QPI. Herein, we introduce a fundamentally new approach by designing QPI contrast agents that allow sensitive detection of intracellular biomolecules. We report a new class of bio-orthogonal QPI-nanoprobes for in situ high-contrast refractive index (RI) imaging of enzyme activity. The nanoprobes feature silica nanoparticles (SiO2 NPs) having higher RI than endogenous cellular components and surface-anchored cyanobenzothiazole-cysteine (CBT-Cys) conjugated enzyme-responsive peptide sequences. The nanoprobes specifically aggregated in cells with target enzyme activity, increasing intracellular RI and enabling precise visualization of intracellular enzyme activity. We envision that this general design of QPI-nanoprobes could open doors for spatial-temporal mapping of enzyme activity with direct implications for disease diagnosis and evaluating the therapeutic efficacy.
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Affiliation(s)
- Swati Tanwar
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Lintong Wu
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Noah Zahn
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Piyush Raj
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Behnaz Ghaemi
- The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University, School of Medicine, Baltimore, Maryland 21205, USA
- Cellular Imaging Section and Vascular Biology Program, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Arnab Chatterjee
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Jeff W M Bulte
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
- The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University, School of Medicine, Baltimore, Maryland 21205, USA
- Cellular Imaging Section and Vascular Biology Program, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
- F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Inc., Baltimore, Maryland 21205, USA
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Ishan Barman
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
- The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University, School of Medicine, Baltimore, Maryland 21205, USA
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
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16
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Lee C, Hugonnet H, Park J, Lee MJ, Park W, Park Y. Single-shot refractive index slice imaging using spectrally multiplexed optical transfer function reshaping. OPTICS EXPRESS 2023; 31:13806-13816. [PMID: 37157259 DOI: 10.1364/oe.485559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The refractive index (RI) of cells and tissues is crucial in pathophysiology as a noninvasive and quantitative imaging contrast. Although its measurements have been demonstrated using three-dimensional quantitative phase imaging methods, these methods often require bulky interferometric setups or multiple measurements, which limits the measurement sensitivity and speed. Here, we present a single-shot RI imaging method that visualizes the RI of the in-focus region of a sample. By exploiting spectral multiplexing and optical transfer function engineering, three color-coded intensity images of a sample with three optimized illuminations were simultaneously obtained in a single-shot measurement. The measured intensity images were then deconvoluted to obtain the RI image of the in-focus slice of the sample. As a proof of concept, a setup was built using Fresnel lenses and a liquid-crystal display. For validation purposes, we measured microspheres of known RI and cross-validated the results with simulated results. Various static and highly dynamic biological cells were imaged to demonstrate that the proposed method can conduct single-shot RI slice imaging of biological samples with subcellular resolution.
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17
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Lee M, Hugonnet H, Lee MJ, Cho Y, Park Y. Optical trapping with holographically structured light for single-cell studies. BIOPHYSICS REVIEWS 2023; 4:011302. [PMID: 38505814 PMCID: PMC10903426 DOI: 10.1063/5.0111104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/25/2022] [Indexed: 03/21/2024]
Abstract
A groundbreaking work in 1970 by Arthur Ashkin paved the way for developing various optical trapping techniques. Optical tweezers have become an established method for the manipulation of biological objects, due to their noninvasiveness and precise controllability. Recent innovations are accelerating and now enable single-cell manipulation through holographic light structuring. In this review, we provide an overview of recent advances in optical tweezer techniques for studies at the individual cell level. Our review focuses on holographic optical tweezers that utilize active spatial light modulators to noninvasively manipulate live cells. The versatility of the technology has led to valuable integrations with microscopy, microfluidics, and biotechnological techniques for various single-cell studies. We aim to recapitulate the basic principles of holographic optical tweezers, highlight trends in their biophysical applications, and discuss challenges and future prospects.
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18
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Chen X, Kandel ME, He S, Hu C, Lee YJ, Sullivan K, Tracy G, Chung HJ, Kong HJ, Anastasio M, Popescu G. Artificial confocal microscopy for deep label-free imaging. NATURE PHOTONICS 2023; 17:250-258. [PMID: 37143962 PMCID: PMC10153546 DOI: 10.1038/s41566-022-01140-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/01/2022] [Indexed: 05/06/2023]
Abstract
Widefield microscopy of optically thick specimens typically features reduced contrast due to "spatial crosstalk", in which the signal at each point in the field of view is the result of a superposition from neighbouring points that are simultaneously illuminated. In 1955, Marvin Minsky proposed confocal microscopy as a solution to this problem. Today, laser scanning confocal fluorescence microscopy is broadly used due to its high depth resolution and sensitivity, but comes at the price of photobleaching, chemical, and photo-toxicity. Here, we present artificial confocal microscopy (ACM) to achieve confocal-level depth sectioning, sensitivity, and chemical specificity, on unlabeled specimens, nondestructively. We equipped a commercial laser scanning confocal instrument with a quantitative phase imaging module, which provides optical path-length maps of the specimen in the same field of view as the fluorescence channel. Using pairs of phase and fluorescence images, we trained a convolution neural network to translate the former into the latter. The training to infer a new tag is very practical as the input and ground truth data are intrinsically registered, and the data acquisition is automated. The ACM images present significantly stronger depth sectioning than the input (phase) images, enabling us to recover confocal-like tomographic volumes of microspheres, hippocampal neurons in culture, and 3D liver cancer spheroids. By training on nucleus-specific tags, ACM allows for segmenting individual nuclei within dense spheroids for both cell counting and volume measurements. In summary, ACM can provide quantitative, dynamic data, nondestructively from thick samples, while chemical specificity is recovered computationally.
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Affiliation(s)
- Xi Chen
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Currently with School of Applied and Engineering Physics, Cornell University, Ithaca, USA
| | - Mikhail E. Kandel
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Currently with Groq, 400 Castro St., Suite 600, Mountain View, CA 94041, USA
| | - Shenghua He
- Department of Computer Science & Engineering, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Chenfei Hu
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Young Jae Lee
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kathryn Sullivan
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gregory Tracy
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hee Jung Chung
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hyun Joon Kong
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mark Anastasio
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gabriel Popescu
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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19
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Wills JW, Robertson J, Tourlomousis P, Gillis CM, Barnes CM, Miniter M, Hewitt RE, Bryant CE, Summers HD, Powell JJ, Rees P. Label-free cell segmentation of diverse lymphoid tissues in 2D and 3D. CELL REPORTS METHODS 2023; 3:100398. [PMID: 36936072 PMCID: PMC10014308 DOI: 10.1016/j.crmeth.2023.100398] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 10/14/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023]
Abstract
Unlocking and quantifying fundamental biological processes through tissue microscopy requires accurate, in situ segmentation of all cells imaged. Currently, achieving this is complex and requires exogenous fluorescent labels that occupy significant spectral bandwidth, increasing the duration and complexity of imaging experiments while limiting the number of channels remaining to address the study's objectives. We demonstrate that the excitation light reflected during routine confocal microscopy contains sufficient information to achieve accurate, label-free cell segmentation in 2D and 3D. This is achieved using a simple convolutional neural network trained to predict the probability that reflected light pixels belong to either nucleus, cytoskeleton, or background classifications. We demonstrate the approach across diverse lymphoid tissues and provide video tutorials demonstrating deployment in Python and MATLAB or via standalone software for Windows.
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Affiliation(s)
- John W. Wills
- Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK
- Department of Biomedical Engineering, Swansea University, Fabian Way, Crymlyn Burrows, Swansea SA1 8EN, Wales, UK
| | - Jack Robertson
- Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK
| | - Pani Tourlomousis
- Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK
| | - Clare M.C. Gillis
- Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK
| | - Claire M. Barnes
- Department of Biomedical Engineering, Swansea University, Fabian Way, Crymlyn Burrows, Swansea SA1 8EN, Wales, UK
| | - Michelle Miniter
- Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK
| | - Rachel E. Hewitt
- Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK
| | - Clare E. Bryant
- Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK
| | - Huw D. Summers
- Department of Biomedical Engineering, Swansea University, Fabian Way, Crymlyn Burrows, Swansea SA1 8EN, Wales, UK
| | - Jonathan J. Powell
- Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK
| | - Paul Rees
- Department of Biomedical Engineering, Swansea University, Fabian Way, Crymlyn Burrows, Swansea SA1 8EN, Wales, UK
- Imaging Platform, Broad Institute of MIT and Harvard, 415 Main Street, Boston, Cambridge, MA 02142, USA
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20
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Ong JJY, Oh J, Yong Ang X, Naidu R, Chu TTT, Hyoung Im J, Manzoor U, Kha Nguyen T, Na SW, Han ET, Davis C, Sun Park W, Chun W, Jun H, Jin Lee S, Na S, Chan JKY, Park Y, Russell B, Chandramohanadas R, Han JH. Optical diffraction tomography and image reconstruction to measure host cell alterations caused by divergent Plasmodium species. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 286:122026. [PMID: 36395614 DOI: 10.1016/j.saa.2022.122026] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/29/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Malaria is a life-threatening infectious disease caused by parasites of the genus Plasmodium. Understanding the biological features of various parasite forms is important for the optical diagnosis and defining pathological states, which are often constrained by the lack of ambient visualization approaches. Here, we employ a label-free tomographic technique to visualize the host red blood cell (RBC) remodeling process and quantify changes in biochemical properties arising from parasitization. Through this, we provide a quantitative body of information pertaining to the influence of host cell environment on growth, survival, and replication of P. falciparum and P. vivax in their respective host cells: mature erythrocytes and young reticulocytes. These exquisite three-dimensional measurements of infected red cells demonstrats the potential of evolving 3D imaging to advance our understanding of Plasmodium biology and host-parasite interactions.
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Affiliation(s)
- Jessica J Y Ong
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Jeonghun Oh
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Xiang Yong Ang
- Department of Microbiology and Immunology, National University of Singapore, Singapore
| | - Renugah Naidu
- Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore, Singapore
| | - Trang T T Chu
- Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore, Singapore
| | - Jae Hyoung Im
- Department of Infectious Disease, Inha University School of Medicine, Incheon 22212, Republic of Korea
| | - Umar Manzoor
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Tuyet Kha Nguyen
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Seok-Won Na
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Christeen Davis
- DBT Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Won Sun Park
- Department of Physiology, School of Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Wanjoo Chun
- Department of Pharmacology, School of Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hojong Jun
- Department of Tropical Medicine, Inha University College of Medicine, Incheon 22212, Republic of Korea
| | - Se Jin Lee
- Department of Obstetrics and Gynecology, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon 24341, South Korea
| | - Sunghun Na
- Department of Obstetrics and Gynecology, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon 24341, South Korea
| | - Jerry K Y Chan
- KK Womens' and Childrens' Hospital, Singapore; Academic Clinical Program in Obstetrics and Gynaecology, Duke-NUS Medical School, 169857, Singapore
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea; Tomocube Inc, Daejeon 34109, Republic of Korea
| | - Bruce Russell
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Rajesh Chandramohanadas
- Department of Microbiology and Immunology, National University of Singapore, Singapore; Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore, Singapore; DBT Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
| | - Jin-Hee Han
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand; Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea.
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21
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Lee D, Lee M, Kwak H, Kim YS, Shim J, Jung JH, Park WS, Park JH, Lee S, Park Y. High-fidelity optical diffraction tomography of live organisms using iodixanol refractive index matching. BIOMEDICAL OPTICS EXPRESS 2022; 13:6404-6415. [PMID: 36589574 PMCID: PMC9774853 DOI: 10.1364/boe.465066] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 10/25/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
Optical diffraction tomography (ODT) enables the three-dimensional (3D) refractive index (RI) reconstruction. However, when the RI difference between a sample and a medium increases, the effects of light scattering become significant, preventing the acquisition of high-quality and accurate RI reconstructions. Herein, we present a method for high-fidelity ODT by introducing non-toxic RI matching media. Optimally reducing the RI contrast enhances the fidelity and accuracy of 3D RI reconstruction, enabling visualization of the morphology and intra-organization of live biological samples without producing toxic effects. We validate our method using various biological organisms, including C. albicans and C. elegans.
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Affiliation(s)
- Dohyeon Lee
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Moosung Lee
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Haechan Kwak
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Young Seo Kim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Jaehyu Shim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Jik Han Jung
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Wei-sun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Ji-Ho Park
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Sumin Lee
- Tomocube Inc., Daejeon 34109, Republic of Korea
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Tomocube Inc., Daejeon 34109, Republic of Korea
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22
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Wei Z, Liu X, Yan R, Sun G, Yu W, Liu Q, Guo Q. Pixel-level multimodal fusion deep networks for predicting subcellular organelle localization from label-free live-cell imaging. Front Genet 2022; 13:1002327. [PMID: 36386823 PMCID: PMC9644055 DOI: 10.3389/fgene.2022.1002327] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/26/2022] [Indexed: 01/25/2023] Open
Abstract
Complex intracellular organizations are commonly represented by dividing the metabolic process of cells into different organelles. Therefore, identifying sub-cellular organelle architecture is significant for understanding intracellular structural properties, specific functions, and biological processes in cells. However, the discrimination of these structures in the natural organizational environment and their functional consequences are not clear. In this article, we propose a new pixel-level multimodal fusion (PLMF) deep network which can be used to predict the location of cellular organelle using label-free cell optical microscopy images followed by deep-learning-based automated image denoising. It provides valuable insights that can be of tremendous help in improving the specificity of label-free cell optical microscopy by using the Transformer-Unet network to predict the ground truth imaging which corresponds to different sub-cellular organelle architectures. The new prediction method proposed in this article combines the advantages of a transformer's global prediction and CNN's local detail analytic ability of background features for label-free cell optical microscopy images, so as to improve the prediction accuracy. Our experimental results showed that the PLMF network can achieve over 0.91 Pearson's correlation coefficient (PCC) correlation between estimated and true fractions on lung cancer cell-imaging datasets. In addition, we applied the PLMF network method on the cell images for label-free prediction of several different subcellular components simultaneously, rather than using several fluorescent labels. These results open up a new way for the time-resolved study of subcellular components in different cells, especially for cancer cells.
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Affiliation(s)
- Zhihao Wei
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, China
| | - Xi Liu
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, China
| | - Ruiqing Yan
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, China
| | - Guocheng Sun
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, China,School of Mechanical Engineering & Hydrogen Energy Research Centre, Beijing Institute of Petrochemical Technology, Beijing, China
| | - Weiyong Yu
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, China
| | - Qiang Liu
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, China
| | - Qianjin Guo
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, China,School of Mechanical Engineering & Hydrogen Energy Research Centre, Beijing Institute of Petrochemical Technology, Beijing, China,*Correspondence: Qianjin Guo,
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23
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Szittner Z, Péter B, Kurunczi S, Székács I, Horváth R. Functional blood cell analysis by label-free biosensors and single-cell technologies. Adv Colloid Interface Sci 2022; 308:102727. [DOI: 10.1016/j.cis.2022.102727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/25/2022] [Accepted: 06/27/2022] [Indexed: 11/01/2022]
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24
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Kim G, Ahn D, Kang M, Park J, Ryu D, Jo Y, Song J, Ryu JS, Choi G, Chung HJ, Kim K, Chung DR, Yoo IY, Huh HJ, Min HS, Lee NY, Park Y. Rapid species identification of pathogenic bacteria from a minute quantity exploiting three-dimensional quantitative phase imaging and artificial neural network. LIGHT, SCIENCE & APPLICATIONS 2022; 11:190. [PMID: 35739098 PMCID: PMC9226356 DOI: 10.1038/s41377-022-00881-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 06/03/2022] [Accepted: 06/09/2022] [Indexed: 05/14/2023]
Abstract
The healthcare industry is in dire need of rapid microbial identification techniques for treating microbial infections. Microbial infections are a major healthcare issue worldwide, as these widespread diseases often develop into deadly symptoms. While studies have shown that an early appropriate antibiotic treatment significantly reduces the mortality of an infection, this effective treatment is difficult to practice. The main obstacle to early appropriate antibiotic treatments is the long turnaround time of the routine microbial identification, which includes time-consuming sample growth. Here, we propose a microscopy-based framework that identifies the pathogen from single to few cells. Our framework obtains and exploits the morphology of the limited sample by incorporating three-dimensional quantitative phase imaging and an artificial neural network. We demonstrate the identification of 19 bacterial species that cause bloodstream infections, achieving an accuracy of 82.5% from an individual bacterial cell or cluster. This performance, comparable to that of the gold standard mass spectroscopy under a sufficient amount of sample, underpins the effectiveness of our framework in clinical applications. Furthermore, our accuracy increases with multiple measurements, reaching 99.9% with seven different measurements of cells or clusters. We believe that our framework can serve as a beneficial advisory tool for clinicians during the initial treatment of infections.
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Affiliation(s)
- Geon Kim
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
| | - Daewoong Ahn
- Tomocube Inc., Daejeon, 34109, Republic of Korea
| | - Minhee Kang
- Smart Healthcare & Device Research Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Jinho Park
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
| | - DongHun Ryu
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
| | - YoungJu Jo
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
- Tomocube Inc., Daejeon, 34109, Republic of Korea
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
| | - Jinyeop Song
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jea Sung Ryu
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Gunho Choi
- Tomocube Inc., Daejeon, 34109, Republic of Korea
| | - Hyun Jung Chung
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Kyuseok Kim
- Department of Emergency Medicine, Bundang CHA Hospital, Seongnam-si, Gyeonggi-Do, 13496, Korea
| | - Doo Ryeon Chung
- Division of Infectious Diseases, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - In Young Yoo
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | | | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea.
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea.
- Tomocube Inc., Daejeon, 34109, Republic of Korea.
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25
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A Novel Peptide-MHC Targeted Chimeric Antigen Receptor T Cell Forms a T Cell-like Immune Synapse. Biomedicines 2021; 9:biomedicines9121875. [PMID: 34944696 PMCID: PMC8699022 DOI: 10.3390/biomedicines9121875] [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: 11/14/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 11/17/2022] Open
Abstract
Chimeric Antigen Receptor (CAR) T cell therapy is a promising form of adoptive cell therapy that re-engineers patient-derived T cells to express a hybrid receptor specific to a tumour-specific antigen of choice. Many well-characterised tumour antigens are intracellular and therefore not accessible to antibodies at the cell surface. Therefore, the ability to target peptide-MHC tumour targets with antibodies is key for wider applicability of CAR T cell therapy in cancer. One way to evaluate the effectiveness and efficiency of ligating tumour target cells is studying the immune synapse. Here we generated a second-generation CAR to targeting the HLA-A*02:01 restricted H3.3K27M epitope, identified as a possible therapeutic target in ~75% of diffuse midline gliomas, used as a model antigen to study the immune synapse. The pMHCI-specific CAR demonstrated specificity, potent activation, cytokine secretion and cytotoxic function. Furthermore, we characterised killing kinetics using live cell imaging as well as CAR synapse confocal imaging. Here we provide evidence of robust CAR targeting of a model peptide-MHC antigen and that, in contrast to protein-specific CARs, these CARs form a TCR-like immune synapse which facilitates TCR-like killing kinetics.
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26
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Mueller K, Saha K. Single Cell Technologies to Dissect Heterogenous Immune Cell Therapy Products. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021; 20:100343. [PMID: 34957355 PMCID: PMC8693636 DOI: 10.1016/j.cobme.2021.100343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Single cell tools have dramatically transformed the life sciences; concurrently, autologous and allogeneic immune cell therapies have recently entered the clinic. Here we discuss methods, applications, and considerations for single cell technologies in the context of immune cell manufacturing. Molecular heterogeneity can be profiled at the level of the genome, epigenome, transcriptome, proteome, metabolome, and antigen receptor repertoire, in isolation or in tandem through multi-omic approaches. Such data inform heterogeneity within cell products and can be linked to potency readouts and clinical data, with the ultimate goal of identifying Critical Quality Attributes to predict patient outcomes. Non-destructive approaches hold promise for monitoring cell state and analyzing the impacts of gene edits within engineered products. Destructive omics approaches could be combined with non-destructive technologies to predict therapeutic potency. These technologies are poised to redefine cell manufacturing toward rapid, cost-effective, and high-throughput methods to detect and respond to dynamic cell states.
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Affiliation(s)
- Katherine Mueller
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin
| | - Krishanu Saha
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin
- Grainger Institute for Engineering, University of Wisconsin-Madison, Madison, Wisconsin
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27
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Roadmap on Digital Holography-Based Quantitative Phase Imaging. J Imaging 2021; 7:jimaging7120252. [PMID: 34940719 PMCID: PMC8703719 DOI: 10.3390/jimaging7120252] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 12/02/2022] Open
Abstract
Quantitative Phase Imaging (QPI) provides unique means for the imaging of biological or technical microstructures, merging beneficial features identified with microscopy, interferometry, holography, and numerical computations. This roadmap article reviews several digital holography-based QPI approaches developed by prominent research groups. It also briefly discusses the present and future perspectives of 2D and 3D QPI research based on digital holographic microscopy, holographic tomography, and their applications.
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28
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Lee AJ, Yoon D, Han S, Hugonnet H, Park W, Park JK, Nam Y, Park Y. Label-free monitoring of 3D cortical neuronal growth in vitro using optical diffraction tomography. BIOMEDICAL OPTICS EXPRESS 2021; 12:6928-6939. [PMID: 34858689 PMCID: PMC8606138 DOI: 10.1364/boe.439404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 05/10/2023]
Abstract
The highly complex central nervous systems of mammals are often studied using three-dimensional (3D) in vitro primary neuronal cultures. A coupled confocal microscopy and immunofluorescence labeling are widely utilized for visualizing the 3D structures of neurons. However, this requires fixation of the neurons and is not suitable for monitoring an identical sample at multiple time points. Thus, we propose a label-free monitoring method for 3D neuronal growth based on refractive index tomograms obtained by optical diffraction tomography. The 3D morphology of the neurons was clearly visualized, and the developmental processes of neurite outgrowth in 3D spaces were analyzed for individual neurons.
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Affiliation(s)
- Ariel J Lee
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Current Affiliation: Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Contributed equally
| | - DongJo Yoon
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea
- Contributed equally
| | - SeungYun Han
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Current Affiliation: Department of Applied Physics, Yale University, New Haven, CT 06520, USA
- Contributed equally
| | - Herve Hugonnet
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - WeiSun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Je-Kyun Park
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - YoonKey Nam
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Tomocube Inc., Daejeon, Republic of Korea
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29
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Liguori F, Amadio S, Volonté C. Fly for ALS: Drosophila modeling on the route to amyotrophic lateral sclerosis modifiers. Cell Mol Life Sci 2021; 78:6143-6160. [PMID: 34322715 PMCID: PMC11072332 DOI: 10.1007/s00018-021-03905-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 12/11/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a rare, devastating disease, causing movement impairment, respiratory failure and ultimate death. A plethora of genetic, cellular and molecular mechanisms are involved in ALS signature, although the initiating causes and progressive pathological events are far from being understood. Drosophila research has produced seminal discoveries for more than a century and has been successfully used in the past 25 years to untangle the process of ALS pathogenesis, and recognize potential markers and novel strategies for therapeutic solutions. This review will provide an updated view of several ALS modifiers validated in C9ORF72, SOD1, FUS, TDP-43 and Ataxin-2 Drosophila models. We will discuss basic and preclinical findings, illustrating recent developments and novel breakthroughs, also depicting unsettled challenges and limitations in the Drosophila-ALS field. We intend to stimulate a renewed debate on Drosophila as a screening route to identify more successful disease modifiers and neuroprotective agents.
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Affiliation(s)
- Francesco Liguori
- Preclinical Neuroscience, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 65, 00143, Rome, Italy
| | - Susanna Amadio
- Preclinical Neuroscience, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 65, 00143, Rome, Italy
| | - Cinzia Volonté
- Preclinical Neuroscience, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 65, 00143, Rome, Italy.
- Institute for Systems Analysis and Computer Science "A. Ruberti", National Research Council (IASI-CNR), Via dei Taurini 19, 00185, Rome, Italy.
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30
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Banerjee R, Shah N, Dicker AP. Next-Generation Implementation of Chimeric Antigen Receptor T-Cell Therapy Using Digital Health. JCO Clin Cancer Inform 2021; 5:668-678. [PMID: 34110929 DOI: 10.1200/cci.21.00023] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Chimeric antigen receptor T-cell (CAR-T) therapy is a paradigm-shifting immunotherapy modality in oncology; however, unique toxicities such as cytokine release syndrome (CRS) and immune effector cell-associated neurotoxicity syndrome limit its ability to be implemented more widely in the outpatient setting or at smaller-volume centers. Three operational challenges with CAR-T therapy include the following: (1) the logistics of toxicity monitoring, ie, with frequent vital sign checks and neurologic assessments; (2) the specialized knowledge required for toxicity management, particularly with regard to CRS and immune effector cell-associated neurotoxicity syndrome; and (3) the need for high-quality symptomatic and supportive care during this intensive period. In this review, we explore potential niches for digital innovations that can improve the implementation of CAR-T therapy in each of these domains. These tools include patient-facing technologies and provider-facing platforms: for example, wearable devices and mobile health apps to screen for fevers and encephalopathy, electronic patient-reported outcome assessments-based workflows to assist with symptom management, machine learning algorithms to predict emerging CRS in real time, clinical decision support systems to assist with toxicity management, and digital coaching to help maintain wellness. Televisits, which have grown in prominence since the novel coronavirus pandemic, will continue to play a key role in the monitoring and management of CAR-T-related toxicities as well. Limitations of these strategies include the need to ensure care equity and stakeholder buy-in, both operationally and financially. Nevertheless, once developed and validated, the next-generation implementation of CAR-T therapy using these digital tools may improve both its safety and accessibility.
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Affiliation(s)
- Rahul Banerjee
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA
| | - Nina Shah
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA
| | - Adam P Dicker
- Department of Radiation Oncology, Jefferson University, Philadelphia, PA.,Jefferson Center for Digital Health, Jefferson University, Philadelphia, PA
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31
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Lee M, Kim K, Oh J, Park Y. Isotropically resolved label-free tomographic imaging based on tomographic moulds for optical trapping. LIGHT, SCIENCE & APPLICATIONS 2021; 10:102. [PMID: 33994544 PMCID: PMC8126562 DOI: 10.1038/s41377-021-00535-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 04/06/2021] [Accepted: 04/14/2021] [Indexed: 05/13/2023]
Abstract
A major challenge in three-dimensional (3D) microscopy is to obtain accurate spatial information while simultaneously keeping the microscopic samples in their native states. In conventional 3D microscopy, axial resolution is inferior to spatial resolution due to the inaccessibility to side scattering signals. In this study, we demonstrate the isotropic microtomography of free-floating samples by optically rotating a sample. Contrary to previous approaches using optical tweezers with multiple foci which are only applicable to simple shapes, we exploited 3D structured light traps that can stably rotate freestanding complex-shaped microscopic specimens, and side scattering information is measured at various sample orientations to achieve isotropic resolution. The proposed method yields an isotropic resolution of 230 nm and captures structural details of colloidal multimers and live red blood cells, which are inaccessible using conventional tomographic microscopy. We envision that the proposed approach can be deployed for solving diverse imaging problems that are beyond the examples shown here.
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Affiliation(s)
- Moosung Lee
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, South Korea
| | - Kyoohyun Kim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
- Max Planck Institute for the Science of Light & Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
| | - Jeonghun Oh
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, South Korea
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea.
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, South Korea.
- Tomocube Inc., Daejeon, 34109, South Korea.
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32
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Ma T, Kong M. Interleukin-18 and -10 may be associated with lymph node metastasis in breast cancer. Oncol Lett 2021; 21:253. [PMID: 33664817 PMCID: PMC7882877 DOI: 10.3892/ol.2021.12515] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 01/06/2021] [Indexed: 12/09/2022] Open
Abstract
Reports on the expression of interleukin (IL)-10 in breast cancer are rare. The present study investigated the correlation between IL-18 and −10 in breast cancer, and assessed their clinical significance. Breast cancer (n=104) and breast fibroadenoma (n=31) tissues that were surgically removed and pathologically confirmed at Jinan Central Hospital Affiliated to Shandong University (Jinan, China) between November 2016 and January 2019 were collected. The expression of IL-18 and −10 was observed via immunohistochemistry. Breast cancer tissues were positive for IL-18 expression, which was primarily located in the cell membrane and cytoplasm. A significant difference in IL-18 expression was observed between breast cancer and fibroadenoma tissues (75.0 vs. 19.4%; P<0.001). IL-10 was expressed in breast cancer tissues and primarily located in the cytoplasm. Breast cancer tissues showed a significantly higher level of IL-10 expression compared with breast fibroadenoma tissues (78.8 vs. 22.6%; P<0.001). The regions of positive IL-18 and −10 expression were consistent. Tissues with positive expression of IL-18 and/or −10 had a significantly higher rate of lymph node metastasis than those with negative expression (IL-18: 67.9 vs. 42.3%; P=0.035; and IL-10: 67.1 vs. 40.9%; P=0.047). In conclusion, IL-18 is highly expressed in breast cancer and correlates positively with IL-10. Both IL-18 and −10 may correlate positively with lymph node metastasis in breast cancer.
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Affiliation(s)
- Teng Ma
- Department of Internal Medicine, The Fifth People's Hospital of Jinan, Jinan, Shandong 250000, P.R. China
| | - Meng Kong
- Department of General Surgery, Qilu Children's Hospital of Shandong University, Jinan, Shandong 250022, P.R. China
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