1
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Jiang X, Peng Z, Zhang J. Starting with screening strains to construct synthetic microbial communities (SynComs) for traditional food fermentation. Food Res Int 2024; 190:114557. [PMID: 38945561 DOI: 10.1016/j.foodres.2024.114557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/16/2024] [Accepted: 05/26/2024] [Indexed: 07/02/2024]
Abstract
With the elucidation of community structures and assembly mechanisms in various fermented foods, core communities that significantly influence or guide fermentation have been pinpointed and used for exogenous restructuring into synthetic microbial communities (SynComs). These SynComs simulate ecological systems or function as adjuncts or substitutes in starters, and their efficacy has been widely verified. However, screening and assembly are still the main limiting factors for implementing theoretic SynComs, as desired strains cannot be effectively obtained and integrated. To expand strain screening methods suitable for SynComs in food fermentation, this review summarizes the recent research trends in using SynComs to study community evolution or interaction and improve the quality of food fermentation, as well as the specific process of constructing synthetic communities. The potential for novel screening modalities based on genes, enzymes and metabolites in food microbial screening is discussed, along with the emphasis on strategies to optimize assembly for facilitating the development of synthetic communities.
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Affiliation(s)
- Xinyi Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zheng Peng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China.
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2
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Ghosh G, Shannon AE, Searle BC. Data acquisition approaches for single cell proteomics. Proteomics 2024:e2400022. [PMID: 39088833 DOI: 10.1002/pmic.202400022] [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: 05/18/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 08/03/2024]
Abstract
Single-cell proteomics (SCP) aims to characterize the proteome of individual cells, providing insights into complex biological systems. It reveals subtle differences in distinct cellular populations that bulk proteome analysis may overlook, which is essential for understanding disease mechanisms and developing targeted therapies. Mass spectrometry (MS) methods in SCP allow the identification and quantification of thousands of proteins from individual cells. Two major challenges in SCP are the limited material in single-cell samples necessitating highly sensitive analytical techniques and the efficient processing of samples, as each biological sample requires thousands of single cell measurements. This review discusses MS advancements to mitigate these challenges using data-dependent acquisition (DDA) and data-independent acquisition (DIA). Additionally, we examine the use of short liquid chromatography gradients and sample multiplexing methods that increase the sample throughput and scalability of SCP experiments. We believe these methods will pave the way for improving our understanding of cellular heterogeneity and its implications for systems biology.
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Affiliation(s)
- Gautam Ghosh
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Ariana E Shannon
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
- Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, Ohio, USA
| | - Brian C Searle
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
- Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, Ohio, USA
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3
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Alayoubi Y, Bentsen M, Looso M. Scanpro is a tool for robust proportion analysis of single-cell resolution data. Sci Rep 2024; 14:15581. [PMID: 38971877 PMCID: PMC11227528 DOI: 10.1038/s41598-024-66381-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 07/01/2024] [Indexed: 07/08/2024] Open
Abstract
In higher organisms, individual cells respond to signals and perturbations by epigenetic regulation and transcriptional adaptation. However, in addition to shifting the expression level of individual genes, the adaptive response of cells can also lead to shifts in the proportions of different cell types. Recent methods such as scRNA-seq allow for the interrogation of expression on the single-cell level, and can quantify individual cell type clusters within complex tissue samples. In order to identify clusters showing differential composition between different biological conditions, differential proportion analysis has recently been introduced. However, bioinformatics tools for robust proportion analysis of both replicated and unreplicated single-cell datasets are critically missing. In this manuscript, we present Scanpro, a modular tool for proportion analysis, seamlessly integrating into widely accepted frameworks in the Python environment. Scanpro is fast, accurate, supports datasets without replicates, and is intended to be used by bioinformatics experts and beginners alike.
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Affiliation(s)
- Yousef Alayoubi
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mette Bentsen
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany.
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4
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Peeters F, Cappuyns S, Piqué-Gili M, Phillips G, Verslype C, Lambrechts D, Dekervel J. Applications of single-cell multi-omics in liver cancer. JHEP Rep 2024; 6:101094. [PMID: 39022385 PMCID: PMC11252522 DOI: 10.1016/j.jhepr.2024.101094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/18/2024] [Accepted: 03/27/2024] [Indexed: 07/20/2024] Open
Abstract
Primary liver cancer, more specifically hepatocellular carcinoma (HCC), remains a significant global health problem associated with increasing incidence and mortality. Clinical, biological, and molecular heterogeneity are well-known hallmarks of cancer and HCC is considered one of the most heterogeneous tumour types, displaying substantial inter-patient, intertumoural and intratumoural variability. This heterogeneity plays a pivotal role in hepatocarcinogenesis, metastasis, relapse and drug response or resistance. Unimodal single-cell sequencing techniques have already revolutionised our understanding of the different layers of molecular hierarchy in the tumour microenvironment of HCC. By highlighting the cellular heterogeneity and the intricate interactions among cancer, immune and stromal cells before and during treatment, these techniques have contributed to a deeper comprehension of tumour clonality, hematogenous spreading and the mechanisms of action of immune checkpoint inhibitors. However, major questions remain to be elucidated, with the identification of biomarkers predicting response or resistance to immunotherapy-based regimens representing an important unmet clinical need. Although the application of single-cell multi-omics in liver cancer research has been limited thus far, a revolution of individualised care for patients with HCC will only be possible by integrating various unimodal methods into multi-omics methodologies at the single-cell resolution. In this review, we will highlight the different established single-cell sequencing techniques and explore their biological and clinical impact on liver cancer research, while casting a glance at the future role of multi-omics in this dynamic and rapidly evolving field.
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Affiliation(s)
- Frederik Peeters
- Digestive Oncology, Department of Gastroenterology, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Clinical Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Centre for Cancer Biology, Leuven, Belgium
| | - Sarah Cappuyns
- Digestive Oncology, Department of Gastroenterology, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Clinical Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Centre for Cancer Biology, Leuven, Belgium
| | - Marta Piqué-Gili
- Liver Cancer Translational Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Gino Phillips
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Centre for Cancer Biology, Leuven, Belgium
| | - Chris Verslype
- Digestive Oncology, Department of Gastroenterology, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Clinical Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Centre for Cancer Biology, Leuven, Belgium
| | - Jeroen Dekervel
- Digestive Oncology, Department of Gastroenterology, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Clinical Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
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5
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Racaniello GF, Silvestri T, Pistone M, D'Amico V, Arduino I, Denora N, Lopedota AA. Innovative Pharmaceutical Techniques for Paediatric Dosage Forms: A Systematic Review on 3D Printing, Prilling/Vibration and Microfluidic Platform. J Pharm Sci 2024; 113:1726-1748. [PMID: 38582283 DOI: 10.1016/j.xphs.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024]
Abstract
The production of paediatric pharmaceutical forms represents a unique challenge within the pharmaceutical industry. The primary goal of these formulations is to ensure therapeutic efficacy, safety, and tolerability in paediatric patients, who have specific physiological needs and characteristics. In recent years, there has been a significant increase in attention towards this area, driven by the need to improve drug administration to children and ensure optimal and specific treatments. Technological innovation has played a crucial role in meeting these requirements, opening new frontiers in the design and production of paediatric pharmaceutical forms. In particular, three emerging technologies have garnered considerable interest and attention within the scientific and industrial community: 3D printing, prilling/vibration, and microfluidics. These technologies offer advanced approaches for the design, production, and customization of paediatric pharmaceutical forms, allowing for more precise dosage modulation, improved solubility, and greater drug acceptability. In this review, we delve into these cutting-edge technologies and their impact on the production of paediatric pharmaceutical forms. We analyse their potential, associated challenges, and recent developments, providing a comprehensive overview of the opportunities that these innovative methodologies offer to the pharmaceutical sector. We examine different pharmaceutical forms generated using these techniques, evaluating their advantages and disadvantages.
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Affiliation(s)
| | - Teresa Silvestri
- Department of Pharmacy, University of Naples Federico II, D. Montesano St. 49, 80131 Naples, Italy
| | - Monica Pistone
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari, Via E. Orabona, 4, 70125, Bari, Italy
| | - Vita D'Amico
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari, Via E. Orabona, 4, 70125, Bari, Italy
| | - Ilaria Arduino
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari, Via E. Orabona, 4, 70125, Bari, Italy
| | - Nunzio Denora
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari, Via E. Orabona, 4, 70125, Bari, Italy.
| | - Angela Assunta Lopedota
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari, Via E. Orabona, 4, 70125, Bari, Italy
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6
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Rasekh M, Harrison S, Schobesberger S, Ertl P, Balachandran W. Reagent storage and delivery on integrated microfluidic chips for point-of-care diagnostics. Biomed Microdevices 2024; 26:28. [PMID: 38825594 DOI: 10.1007/s10544-024-00709-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2024] [Indexed: 06/04/2024]
Abstract
Microfluidic-based point-of-care diagnostics offer several unique advantages over existing bioanalytical solutions, such as automation, miniaturisation, and integration of sensors to rapidly detect on-site specific biomarkers. It is important to highlight that a microfluidic POC system needs to perform a number of steps, including sample preparation, nucleic acid extraction, amplification, and detection. Each of these stages involves mixing and elution to go from sample to result. To address these complex sample preparation procedures, a vast number of different approaches have been developed to solve the problem of reagent storage and delivery. However, to date, no universal method has been proposed that can be applied as a working solution for all cases. Herein, both current self-contained (stored within the chip) and off-chip (stored in a separate device and brought together at the point of use) are reviewed, and their merits and limitations are discussed. This review focuses on reagent storage devices that could be integrated with microfluidic devices, discussing further issues or merits of these storage solutions in two different sections: direct on-chip storage and external storage with their application devices. Furthermore, the different microvalves and micropumps are considered to provide guidelines for designing appropriate integrated microfluidic point-of-care devices.
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Affiliation(s)
- Manoochehr Rasekh
- College of Engineering, Design and Physical Sciences, Brunel University London, Uxbridge, UB8 3PH, UK.
| | - Sam Harrison
- College of Engineering, Design and Physical Sciences, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Silvia Schobesberger
- Faculty of Technical Chemistry, Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060, Vienna, Austria
| | - Peter Ertl
- Faculty of Technical Chemistry, Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060, Vienna, Austria
| | - Wamadeva Balachandran
- College of Engineering, Design and Physical Sciences, Brunel University London, Uxbridge, UB8 3PH, UK.
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7
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Liang L, Liang M, Zuo Z, Ai Y. Label-free single-cell analysis in microdroplets using a light-scattering-based optofluidic chip. Biosens Bioelectron 2024; 253:116148. [PMID: 38428071 DOI: 10.1016/j.bios.2024.116148] [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: 11/16/2023] [Revised: 02/01/2024] [Accepted: 02/19/2024] [Indexed: 03/03/2024]
Abstract
Droplet-based single-cell analysis is a very powerful tool for studying phenotypic and genomic heterogeneity at single-cell resolution for a variety of biological problems. In conventional two-phase droplet microfluidics, due to the mismatch in optical properties between oil and aqueous phases, light scattering mainly happens at the oil/water interface that disables light-scattering-based cell analysis confined in microdroplets. Detection and analysis of cells in microdroplets thus mostly rely on the fluorescence labeling of cell samples, which may suffer from complex operation, cytotoxicity, and low fluorescence stability. In this work, we propose a novel light-scattering-based droplet screening (LSDS) that can effectively detect and characterize single cells confined in droplets by adjusting the optical properties of droplets in a multiangle optofluidic chip. Theoretical and simulated calculations suggest that refractive index (RI) matching in droplet two-phase materials can reduce or eliminate droplets' scattered signals (background signal), enabling the differentiation of scattered signals from single cells and particles within droplets. Furthermore, by using a set of multiangle (from -145° to 140°) optical fibers integrated into the optofluidic chip, the scattered light properties of droplets with the RI ranging from 1.334 to 1.429 are measured. We find that the smaller the RI and size of microparticles inside droplets are, the smaller the RI difference between two-phase materials Δn is required. Especially, when Δn is smaller than 0.02, single cells in droplets can be detected and analyzed solely based on light scattering. This capability allows to accurately detect droplets containing one single cell and one single gel bead, a typical droplet encapsulation for single-cell sequencing. Altogether, this work provides a powerful platform for high-throughput label-free single-cell analysis in microdroplets for diverse single-cell related biological assays.
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Affiliation(s)
- Li Liang
- School of Physics and Electronic Information, Anhui Normal University, Wuhu, 241000, China
| | - Minhui Liang
- Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore, 487372, Singapore
| | - Zewen Zuo
- School of Physics and Electronic Information, Anhui Normal University, Wuhu, 241000, China
| | - Ye Ai
- Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore, 487372, Singapore.
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8
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Hakami N, Burgstaller A, Gao N, Rutz A, Mann S, Staufer O. Functional Integration of Synthetic Cells into 3D Microfluidic Devices for Artificial Organ-On-Chip Technologies. Adv Healthc Mater 2024:e2303334. [PMID: 38794823 DOI: 10.1002/adhm.202303334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 05/10/2024] [Indexed: 05/26/2024]
Abstract
Microfluidics plays a pivotal role in organ-on-chip technologies and in the study of synthetic cells, especially in the development and analysis of artificial cell models. However, approaches that use synthetic cells as integral functional components for microfluidic systems to shape the microenvironment of natural living cells cultured on-chip are not explored. Here, colloidosome-based synthetic cells are integrated into 3D microfluidic devices, pioneering the concept of synthetic cell-based microenvironments for organs-on-chip. Methods are devised to create dense and stable networks of silica colloidosomes, enveloped by supported lipid bilayers, within microfluidic channels. These networks promote receptor-ligand interactions with on-chip cultured cells. Furthermore, a technique is introduced for the controlled release of growth factors from the synthetic cells into the channels, using a calcium alginate-based hydrogel formation within the colloidosomes. To demonstrate the potential of the technology, a modular plug-and-play lymph-node-on-a-chip prototype that guides the expansion of primary human T cells by stimulating receptor ligands on the T cells and modulating their cytokine environment is presented. This integration of synthetic cells into microfluidic systems offers a new direction for organ-on-chip technologies and suggests further avenues for exploration in potential therapeutic applications.
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Affiliation(s)
- Niki Hakami
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
| | - Anna Burgstaller
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
| | - Ning Gao
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Angela Rutz
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
| | - Stephen Mann
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
- Max Planck Bristol Centre for Minimal Biology, School of Chemistry, Bristol, BS8 1TS, UK
| | - Oskar Staufer
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
- Max Planck Bristol Centre for Minimal Biology, School of Chemistry, Bristol, BS8 1TS, UK
- Center for Biophysics, Saarland University, Campus Saarland, 66123, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, Campus E8 1, 66123, Saarbrücken, Germany
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9
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Chernyadiev AV, But DB, Ivonyak Y, Ikamas K, Lisauskas A. A CMOS-integrated terahertz near-field sensor based on an ultra-strongly coupled meta-atom. Sci Rep 2024; 14:11483. [PMID: 38769178 PMCID: PMC11106299 DOI: 10.1038/s41598-024-61971-x] [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: 03/06/2024] [Accepted: 05/13/2024] [Indexed: 05/22/2024] Open
Abstract
Recently, plasmonic-based sensors operating in the terahertz frequency range have emerged as perspective tools for rapid and efficient label-free biosensing applications. In this work, we present a fully electronic approach allowing us to achieve state-of-the-art sensitivity by utilizing a near-field-coupled electronic sensor. We demonstrate that the proposed concept enables the efficient implementation and probing of a so-called ultra-strongly coupled sub-wavelength meta-atom as well as a single resonant circuit, allowing to limit the volume of material under test down to a few picoliter range. The sensor has been monolithically integrated into a cost-efficient silicon-based CMOS technology. Our findings are supported by both numerical and analytical models and validated through experiments. They lay the groundwork for near-future developments, outlining the perspectives for a terahertz microfluidic lab-on-chip dielectric spectroscopy sensor.
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Affiliation(s)
- Alexander V Chernyadiev
- CENTERA Laboratories, Institute of High Pressure Physics PAS, Sokołowska st. 29/37, 01-142, Warsaw, Poland.
| | - Dmytro B But
- CENTERA Laboratories, Institute of High Pressure Physics PAS, Sokołowska st. 29/37, 01-142, Warsaw, Poland
| | - Yurii Ivonyak
- CENTERA Laboratories, Institute of High Pressure Physics PAS, Sokołowska st. 29/37, 01-142, Warsaw, Poland
| | - Kęstutis Ikamas
- Institute of Applied Electrodynamics and Telecommunications, Vilnius University, Saulėtekio av. 9, 10222, Vilnius, Lithuania
| | - Alvydas Lisauskas
- Institute of Applied Electrodynamics and Telecommunications, Vilnius University, Saulėtekio av. 9, 10222, Vilnius, Lithuania.
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10
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Chun J, Moon JH, Kwack KH, Jang EY, Lee S, Kim HK, Lee JH. Single-cell RNA sequencing reveals the heterogeneity of adipose tissue-derived mesenchymal stem cells under chondrogenic induction. BMB Rep 2024; 57:232-237. [PMID: 37915134 PMCID: PMC11139680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 10/03/2023] [Accepted: 10/12/2023] [Indexed: 11/03/2023] Open
Abstract
This study investigated how adipose tissue-derived mesenchymal stem cells (AT-MSCs) respond to chondrogenic induction using droplet-based single-cell RNA sequencing (scRNA-seq). We analyzed 37,219 high-quality transcripts from control cells and cells induced for 1 week (1W) and 2 weeks (2W). Four distinct cell clusters (0-3), undetectable by bulk analysis, exhibited varying proportions. Cluster 1 dominated in control and 1W cells, whereas clusters (3, 2, and 0) exclusively dominated in control, 1W, and 2W cells, respectively. Furthermore, heterogeneous chondrogenic markers expression within clusters emerged. Gene ontology (GO) enrichment analysis of differentially expressed genes unveiled cluster-specific variations in key biological processes (BP): (1) Cluster 1 exhibited up-regulation of GO-BP terms related to ribosome biogenesis and translational control, crucial for maintaining stem cell properties and homeostasis; (2) Additionally, cluster 1 showed up-regulation of GO-BP terms associated with mitochondrial oxidative metabolism; (3) Cluster 3 displayed up-regulation of GO-BP terms related to cell proliferation; (4) Clusters 0 and 2 demonstrated similar up-regulation of GO-BP terms linked to collagen fibril organization and supramolecular fiber organization. However, only cluster 0 showed a significant decrease in GO-BP terms related to ribosome production, implying a potential correlation between ribosome regulation and the differentiation stages of AT-MSCs. Overall, our findings highlight heterogeneous cell clusters with varying balances between proliferation and differentiation before, and after, chondrogenic stimulation. This provides enhanced insights into the single-cell dynamics of AT-MSCs during chondrogenic differentiation. [BMB Reports 2024; 57(5): 232-237].
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Affiliation(s)
- Jeewan Chun
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul 02447, Korea
- Department of Dentistry, Graduate School, Kyung Hee University, Seoul 02447, Korea
| | - Ji-Hoi Moon
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul 02447, Korea
| | - Kyu Hwan Kwack
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul 02447, Korea
| | - Eun-Young Jang
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul 02447, Korea
- Department of Dentistry, Graduate School, Kyung Hee University, Seoul 02447, Korea
| | - Saebyeol Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Hak Kyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Jae-Hyung Lee
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul 02447, Korea
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11
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Duhan L, Kumari D, Naime M, Parmar VS, Chhillar AK, Dangi M, Pasrija R. Single-cell transcriptomics: background, technologies, applications, and challenges. Mol Biol Rep 2024; 51:600. [PMID: 38689046 DOI: 10.1007/s11033-024-09553-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
Single-cell sequencing was developed as a high-throughput tool to elucidate unusual and transient cell states that are barely visible in the bulk. This technology reveals the evolutionary status of cells and differences between populations, helps to identify unique cell subtypes and states, reveals regulatory relationships between genes, targets and molecular mechanisms in disease processes, tumor heterogeneity, the state of the immune environment, etc. However, the high cost and technical limitations of single-cell sequencing initially prevented its widespread application, but with advances in research, numerous new single-cell sequencing techniques have been discovered, lowering the cost barrier. Many single-cell sequencing platforms and bioinformatics methods have recently become commercially available, allowing researchers to make fascinating observations. They are now increasingly being used in various industries. Several protocols have been discovered in this context and each technique has unique characteristics, capabilities and challenges. This review presents the latest advancements in single-cell transcriptomics technologies. This includes single-cell transcriptomics approaches, workflows and statistical approaches to data processing, as well as the potential advances, applications, opportunities and challenges of single-cell transcriptomics technology. You will also get an overview of the entry points for spatial transcriptomics and multi-omics.
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Affiliation(s)
- Lucky Duhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Deepika Kumari
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Mohammad Naime
- Central Research Institute of Unani Medicine (Under Central Council for Research in Unani Medicine, Ministry of Ayush, Govt of India), Uttar Pradesh, Lucknow, India
| | - Virinder S Parmar
- CUNY-Graduate Center and Departments of Chemistry, Nanoscience Program, City College & Medgar Evers College, The City University of New York, 1638 Bedford Avenue, Brooklyn, NY, 11225, USA
- Institute of Click Chemistry Research and Studies, Amity University, Noida, Uttar Pradesh, 201303, India
| | - Anil K Chhillar
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Mehak Dangi
- Centre for Bioinformatics, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Ritu Pasrija
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, 124001, India.
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12
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Tukker AM, Bowman AB. Application of Single Cell Gene Expression Technologies to Neurotoxicology. CURRENT OPINION IN TOXICOLOGY 2024; 37:100458. [PMID: 38617035 PMCID: PMC11008280 DOI: 10.1016/j.cotox.2023.100458] [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] [Indexed: 04/16/2024]
Abstract
Neurotoxicological research faces the challenge of linking biological changes resulting from exposures to neuronal function. An additional challenge is understanding cell-type specific differences and selective vulnerabilities of distinct neuronal populations to toxic insults. Single cell RNA-sequencing (scRNA-seq) allows for measurement of the transcriptome of individual cells. This makes it a valuable tool for validating and characterizing cell types present in multicell type samples in complex tissue or cell culture models, but also for understanding how different cell types respond to toxic insults. Pathway analysis of differentially expressed genes can provide in depth insights into underlying cell type-specific mechanisms of neurotoxicity. Toxicological data often has to be translated to outcomes for human health which requires an understanding of inter-species differences. Transcriptomic data aids in understanding these differences, including understanding developmental timelines of different species. We believe that scRNA-seq holds exciting promises for future neurotoxicological research.
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Affiliation(s)
- Anke M Tukker
- School of Health Sciences, Purdue University, West Lafayette, IN, USA
| | - Aaron B Bowman
- School of Health Sciences, Purdue University, West Lafayette, IN, USA
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Chen Y, Zhou X, Ji L, Zhao J, Xian H, Xu Y, Wang Z, Ge W. Construction and analysis of a joint diagnostic model of machine learning for cryptorchidism based on single-cell sequencing. Birth Defects Res 2024; 116:e2316. [PMID: 38459615 DOI: 10.1002/bdr2.2316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/29/2023] [Accepted: 01/21/2024] [Indexed: 03/10/2024]
Abstract
BACKGROUND Cryptorchidism is a condition in which one or both of a baby's testicles do not fully descend into the bottom of the scrotum. Newborns with cryptorchidism are at increased risk of developing infertility later in life. The aim of this study was to develop a novel diagnostic model for cryptorchidism and to identify new biomarkers associated with cryptorchidism. METHODS The study data were obtained from RNA sequencing data of cryptorchid patients from Nantong University Hospital and the Gene Expression Omnibus (GEO) database. Differential expression analysis was used to obtain differentially expressed genes (DEGs) between the control and cryptorchid groups. These DEGs were analyzed for their functions by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment using GSEA software. Random Forest algorithm was used to screen central genes based on these DEGs. Neuralnet software package was used to develop artificial neural network models. Based on clinical data, receiver operating characteristic (ROC) was used to validate the models. Single-cell sequencing analysis was used for the pathogenesis of cryptorchidism. RESULTS We obtained a total of 525 important DEGs related to cryptorchidism, which are mainly associated with biological functions such as supramolecular complexes and microtubule cytoskeleton. Random forest approach screening obtained eight hub genes. A neural network based on the hub genes showed a 100% success rate of the model. Finally, single-cell sequencing analysis validated the hub genes. CONCLUSION We developed a novel diagnostic model for cryptorchidism using artificial neural networks and validated its utility as an effective diagnostic tool.
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Affiliation(s)
- Yuehua Chen
- Department of Pediatric Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Xiaomeng Zhou
- Department of Pediatric Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Linghua Ji
- Department of Pediatric Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Jun Zhao
- Department of Pediatric Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Hua Xian
- Department of Pediatric Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Yunzhao Xu
- Department of Obstetrics and Gynecology, Affiliated Hospital of Nantong University, Nantong, China
| | - Ziheng Wang
- Department of Clinical Biobank, Affiliated Hospital of Nantong University, Nantong, China
- Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau, China
| | - Wenliang Ge
- Department of Pediatric Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Department of Pediatric Surgery, School of Medicine, Nantong University, Nantong, China
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Jogi HR, Smaraki N, Nayak SS, Rajawat D, Kamothi DJ, Panigrahi M. Single cell RNA-seq: a novel tool to unravel virus-host interplay. Virusdisease 2024; 35:41-54. [PMID: 38817399 PMCID: PMC11133279 DOI: 10.1007/s13337-024-00859-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/12/2024] [Indexed: 06/01/2024] Open
Abstract
Over the last decade, single cell RNA sequencing (scRNA-seq) technology has caught the momentum of being a vital revolutionary tool to unfold cellular heterogeneity by high resolution assessment. It evades the inadequacies of conventional sequencing technology which was able to detect only average expression level among cell populations. In the era of twenty-first century, several epidemic and pandemic viruses have emerged. Being an intracellular entity, viruses totally rely on host. Complex virus-host dynamics result when the virus tend to obtain factors from host cell required for its replication and establishment of infection. As a prevailing tool, scRNA-seq is able to understand virus-host interplay by comprehensive transcriptome profiling. Because of technological and methodological advancement, this technology is capable to recognize viral genome and host cell response heterogeneity. Further development in analytical methods with multiomics approach and increased availability of accessible scRNA-seq datasets will improve the understanding of viral pathogenesis that can be helpful for development of novel antiviral therapeutic strategies.
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Affiliation(s)
- Harsh Rajeshbhai Jogi
- Division of Veterinary Microbiology, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Nabaneeta Smaraki
- Division of Veterinary Microbiology, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Divya Rajawat
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Dhaval J. Kamothi
- Division of Pharmacology and Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
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Enders A, Grünberger A, Bahnemann J. Towards Small Scale: Overview and Applications of Microfluidics in Biotechnology. Mol Biotechnol 2024; 66:365-377. [PMID: 36515858 PMCID: PMC10881759 DOI: 10.1007/s12033-022-00626-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/26/2022] [Indexed: 12/15/2022]
Abstract
Thanks to recent and continuing technological innovations, modern microfluidic systems are increasingly offering researchers working across all fields of biotechnology exciting new possibilities (especially with respect to facilitating high throughput analysis, portability, and parallelization). The advantages offered by microfluidic devices-namely, the substantially lowered chemical and sample consumption they require, the increased energy and mass transfer they offer, and their comparatively small size-can potentially be leveraged in every sub-field of biotechnology. However, to date, most of the reported devices have been deployed in furtherance of healthcare, pharmaceutical, and/or industrial applications. In this review, we consider examples of microfluidic and miniaturized systems across biotechnology sub-fields. In this context, we point out the advantages of microfluidics for various applications and highlight the common features of devices and the potential for transferability to other application areas. This will provide incentives for increased collaboration between researchers from different disciplines in the field of biotechnology.
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Affiliation(s)
- Anton Enders
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 5, 30167, Hannover, Germany
| | - Alexander Grünberger
- Institute of Process Engineering in Life Sciences: Microsystems in Bioprocess Engineering, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131, Karlsruhe, Germany
| | - Janina Bahnemann
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159, Augsburg, Germany.
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Schlotheuber LJ, Lüchtefeld I, Eyer K. Antibodies, repertoires and microdevices in antibody discovery and characterization. LAB ON A CHIP 2024; 24:1207-1225. [PMID: 38165819 PMCID: PMC10898418 DOI: 10.1039/d3lc00887h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/01/2023] [Indexed: 01/04/2024]
Abstract
Therapeutic antibodies are paramount in treating a wide range of diseases, particularly in auto-immunity, inflammation and cancer, and novel antibody candidates recognizing a vast array of novel antigens are needed to expand the usefulness and applications of these powerful molecules. Microdevices play an essential role in this challenging endeavor at various stages since many general requirements of the overall process overlap nicely with the general advantages of microfluidics. Therefore, microfluidic devices are rapidly taking over various steps in the process of new candidate isolation, such as antibody characterization and discovery workflows. Such technologies can allow for vast improvements in time-lines and incorporate conservative antibody stability and characterization assays, but most prominently screenings and functional characterization within integrated workflows due to high throughput and standardized workflows. First, we aim to provide an overview of the challenges of developing new therapeutic candidates, their repertoires and requirements. Afterward, this review focuses on the discovery of antibodies using microfluidic systems, technological aspects of micro devices and small-scale antibody protein characterization and selection, as well as their integration and implementation into antibody discovery workflows. We close with future developments in microfluidic detection and antibody isolation principles and the field in general.
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Affiliation(s)
- Luca Johannes Schlotheuber
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093 Zürich, Switzerland.
| | - Ines Lüchtefeld
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093 Zürich, Switzerland.
- ETH Laboratory for Tumor and Stem Cell Dynamics, Institute of Molecular Health Sciences, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Klaus Eyer
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093 Zürich, Switzerland.
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Qu HQ, Kao C, Hakonarson H. Single-Cell RNA Sequencing Technology Landscape in 2023. Stem Cells 2024; 42:1-12. [PMID: 37934608 DOI: 10.1093/stmcls/sxad077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/29/2023] [Indexed: 11/09/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular heterogeneity and the dynamics of gene expression, bearing profound significance in stem cell research. Depending on the starting materials used for analysis, scRNA-seq encompasses scRNA-seq and single-nucleus RNA sequencing (snRNA-seq). scRNA-seq excels in capturing cellular heterogeneity and characterizing rare cell populations within complex tissues, while snRNA-seq is advantageous in situations where intact cell dissociation is challenging or undesirable (eg, epigenomic studies). A number of scRNA-seq technologies have been developed as of late, including but not limited to droplet-based, plate-based, hydrogel-based, and spatial transcriptomics. The number of cells, sequencing depth, and sequencing length in scRNA-seq can vary across different studies. Addressing current technical challenges will drive the future of scRNA-seq, leading to more comprehensive and precise insights into cellular biology and disease mechanisms informing therapeutic interventions.
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Affiliation(s)
- Hui-Qi Qu
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PAUSA
| | - Charlly Kao
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PAUSA
| | - Hakon Hakonarson
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PAUSA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
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Shah RK, Cygan E, Kozlik T, Colina A, Zamora AE. Utilizing immunogenomic approaches to prioritize targetable neoantigens for personalized cancer immunotherapy. Front Immunol 2023; 14:1301100. [PMID: 38149253 PMCID: PMC10749952 DOI: 10.3389/fimmu.2023.1301100] [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: 09/24/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023] Open
Abstract
Advancements in sequencing technologies and bioinformatics algorithms have expanded our ability to identify tumor-specific somatic mutation-derived antigens (neoantigens). While recent studies have shown neoantigens to be compelling targets for cancer immunotherapy due to their foreign nature and high immunogenicity, the need for increasingly accurate and cost-effective approaches to rapidly identify neoantigens remains a challenging task, but essential for successful cancer immunotherapy. Currently, gene expression analysis and algorithms for variant calling can be used to generate lists of mutational profiles across patients, but more care is needed to curate these lists and prioritize the candidate neoantigens most capable of inducing an immune response. A growing amount of evidence suggests that only a handful of somatic mutations predicted by mutational profiling approaches act as immunogenic neoantigens. Hence, unbiased screening of all candidate neoantigens predicted by Whole Genome Sequencing/Whole Exome Sequencing may be necessary to more comprehensively access the full spectrum of immunogenic neoepitopes. Once putative cancer neoantigens are identified, one of the largest bottlenecks in translating these neoantigens into actionable targets for cell-based therapies is identifying the cognate T cell receptors (TCRs) capable of recognizing these neoantigens. While many TCR-directed screening and validation assays have utilized bulk samples in the past, there has been a recent surge in the number of single-cell assays that provide a more granular understanding of the factors governing TCR-pMHC interactions. The goal of this review is to provide an overview of existing strategies to identify candidate neoantigens using genomics-based approaches and methods for assessing neoantigen immunogenicity. Additionally, applications, prospects, and limitations of some of the current single-cell technologies will be discussed. Finally, we will briefly summarize some of the recent models that have been used to predict TCR antigen specificity and analyze the TCR receptor repertoire.
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Affiliation(s)
- Ravi K. Shah
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Erin Cygan
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Tanya Kozlik
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Alfredo Colina
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Anthony E. Zamora
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
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Han X, Xu X, Yang C, Liu G. Microfluidic design in single-cell sequencing and application to cancer precision medicine. CELL REPORTS METHODS 2023; 3:100591. [PMID: 37725985 PMCID: PMC10545941 DOI: 10.1016/j.crmeth.2023.100591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/01/2023] [Accepted: 08/24/2023] [Indexed: 09/21/2023]
Abstract
Single-cell sequencing (SCS) is a crucial tool to reveal the genetic and functional heterogeneity of tumors, providing unique insights into the clonal evolution, microenvironment, drug resistance, and metastatic progression of cancers. Microfluidics is a critical component of many SCS technologies and workflows, conferring advantages in throughput, economy, and automation. Here, we review the current landscape of microfluidic architectures and sequencing techniques for single-cell omics analysis and highlight how these have enabled recent applications in oncology research. We also discuss the challenges and the promise of microfluidics-based single-cell analysis in the future of precision oncology.
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Affiliation(s)
- Xin Han
- CUHK(SZ)-Boyalife Joint Laboratory of Regenerative Medicine Engineering, Biomedical Engineering Programme, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Xing Xu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China; Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related 12 Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Chaoyang Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China; Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related 12 Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.
| | - Guozhen Liu
- CUHK(SZ)-Boyalife Joint Laboratory of Regenerative Medicine Engineering, Biomedical Engineering Programme, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China.
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Orrapin S, Thongkumkoon P, Udomruk S, Moonmuang S, Sutthitthasakul S, Yongpitakwattana P, Pruksakorn D, Chaiyawat P. Deciphering the Biology of Circulating Tumor Cells through Single-Cell RNA Sequencing: Implications for Precision Medicine in Cancer. Int J Mol Sci 2023; 24:12337. [PMID: 37569711 PMCID: PMC10418766 DOI: 10.3390/ijms241512337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Circulating tumor cells (CTCs) hold unique biological characteristics that directly involve them in hematogenous dissemination. Studying CTCs systematically is technically challenging due to their extreme rarity and heterogeneity and the lack of specific markers to specify metastasis-initiating CTCs. With cutting-edge technology, single-cell RNA sequencing (scRNA-seq) provides insights into the biology of metastatic processes driven by CTCs. Transcriptomics analysis of single CTCs can decipher tumor heterogeneity and phenotypic plasticity for exploring promising novel therapeutic targets. The integrated approach provides a perspective on the mechanisms underlying tumor development and interrogates CTCs interactions with other blood cell types, particularly those of the immune system. This review aims to comprehensively describe the current study on CTC transcriptomic analysis through scRNA-seq technology. We emphasize the workflow for scRNA-seq analysis of CTCs, including enrichment, single cell isolation, and bioinformatic tools applied for this purpose. Furthermore, we elucidated the translational knowledge from the transcriptomic profile of individual CTCs and the biology of cancer metastasis for developing effective therapeutics through targeting key pathways in CTCs.
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Affiliation(s)
- Santhasiri Orrapin
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
| | - Patcharawadee Thongkumkoon
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
| | - Sasimol Udomruk
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
- Musculoskeletal Science and Translational Research (MSTR) Center, Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand
| | - Sutpirat Moonmuang
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
| | - Songphon Sutthitthasakul
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
| | - Petlada Yongpitakwattana
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
| | - Dumnoensun Pruksakorn
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
- Musculoskeletal Science and Translational Research (MSTR) Center, Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand
- Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand
| | - Parunya Chaiyawat
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
- Musculoskeletal Science and Translational Research (MSTR) Center, Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand
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Singh S, Agrawal M, Vashist R, Patel RK, Sangave SD, Alexander A. Recent advancements on in vitro blood-brain barrier model: A reliable and efficient screening approach for preclinical and clinical investigation. Expert Opin Drug Deliv 2023; 20:1839-1857. [PMID: 38100459 DOI: 10.1080/17425247.2023.2295940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/13/2023] [Indexed: 12/17/2023]
Abstract
INTRODUCTION The efficiency of brain therapeutics is greatly hindered by the blood-brain barrier (BBB). BBB's protective function, selective permeability, and dynamic functionality maintain the harmony between the brain and peripheral region. Thus, the design of any novel drug carrier system requires the complete study and investigation of BBB permeability, efflux transport, and the effect of associated cellular and non-vascular unit trafficking on BBB penetrability. The in vitro BBB models offer a most promising, and reliable mode of initial investigation of BBB permeability and associated factors as strong evidence for further preclinical and clinical investigation. AREA COVERED This review work covers the structure and functions of BBB components and different types of in vitro BBB models along with factors affecting BBB model development and model selection criteria. EXPERT OPINION In vivo models assume to reciprocate the physiological environment to the maximum extent. However, the interspecies variability, NVUs trafficking, dynamic behavior of BBB, etc., lead to non-reproducible results. The in vitro models are comparatively less complex, and flexible, as per the study design, could generate substantial evidence and help identify suitable in vivo animal model selection.
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Affiliation(s)
- Snigdha Singh
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Guwahati, India
| | - Mukta Agrawal
- School of Pharmacy and Technology Management, Narsee Monjee Institute of Management Studies, Mahbubnagar, India
| | - Rajat Vashist
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Guwahati, India
| | - Rohit K Patel
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Guwahati, India
| | | | - Amit Alexander
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Guwahati, India
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Tsai HF, Podder S, Chen PY. Microsystem Advances through Integration with Artificial Intelligence. MICROMACHINES 2023; 14:826. [PMID: 37421059 DOI: 10.3390/mi14040826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 07/09/2023]
Abstract
Microfluidics is a rapidly growing discipline that involves studying and manipulating fluids at reduced length scale and volume, typically on the scale of micro- or nanoliters. Under the reduced length scale and larger surface-to-volume ratio, advantages of low reagent consumption, faster reaction kinetics, and more compact systems are evident in microfluidics. However, miniaturization of microfluidic chips and systems introduces challenges of stricter tolerances in designing and controlling them for interdisciplinary applications. Recent advances in artificial intelligence (AI) have brought innovation to microfluidics from design, simulation, automation, and optimization to bioanalysis and data analytics. In microfluidics, the Navier-Stokes equations, which are partial differential equations describing viscous fluid motion that in complete form are known to not have a general analytical solution, can be simplified and have fair performance through numerical approximation due to low inertia and laminar flow. Approximation using neural networks trained by rules of physical knowledge introduces a new possibility to predict the physicochemical nature. The combination of microfluidics and automation can produce large amounts of data, where features and patterns that are difficult to discern by a human can be extracted by machine learning. Therefore, integration with AI introduces the potential to revolutionize the microfluidic workflow by enabling the precision control and automation of data analysis. Deployment of smart microfluidics may be tremendously beneficial in various applications in the future, including high-throughput drug discovery, rapid point-of-care-testing (POCT), and personalized medicine. In this review, we summarize key microfluidic advances integrated with AI and discuss the outlook and possibilities of combining AI and microfluidics.
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Affiliation(s)
- Hsieh-Fu Tsai
- Department of Biomedical Engineering, Chang Gung University, Taoyuan City 333, Taiwan
- Department of Neurosurgery, Chang Gung Memorial Hospital, Keelung, Keelung City 204, Taiwan
- Center for Biomedical Engineering, Chang Gung University, Taoyuan City 333, Taiwan
| | - Soumyajit Podder
- Department of Biomedical Engineering, Chang Gung University, Taoyuan City 333, Taiwan
| | - Pin-Yuan Chen
- Department of Biomedical Engineering, Chang Gung University, Taoyuan City 333, Taiwan
- Department of Neurosurgery, Chang Gung Memorial Hospital, Keelung, Keelung City 204, Taiwan
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Biosensor integrated brain-on-a-chip platforms: Progress and prospects in clinical translation. Biosens Bioelectron 2023; 225:115100. [PMID: 36709589 DOI: 10.1016/j.bios.2023.115100] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 01/07/2023] [Accepted: 01/22/2023] [Indexed: 01/26/2023]
Abstract
Because of the brain's complexity, developing effective treatments for neurological disorders is a formidable challenge. Research efforts to this end are advancing as in vitro systems have reached the point that they can imitate critical components of the brain's structure and function. Brain-on-a-chip (BoC) was first used for microfluidics-based systems with small synthetic tissues but has expanded recently to include in vitro simulation of the central nervous system (CNS). Defining the system's qualifying parameters may improve the BoC for the next generation of in vitro platforms. These parameters show how well a given platform solves the problems unique to in vitro CNS modeling (like recreating the brain's microenvironment and including essential parts like the blood-brain barrier (BBB)) and how much more value it offers than traditional cell culture systems. This review provides an overview of the practical concerns of creating and deploying BoC systems and elaborates on how these technologies might be used. Not only how advanced biosensing technologies could be integrated with BoC system but also how novel approaches will automate assays and improve point-of-care (PoC) diagnostics and accurate quantitative analyses are discussed. Key challenges providing opportunities for clinical translation of BoC in neurodegenerative disorders are also addressed.
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Back to Basics: A Simplified Improvement to Multiple Displacement Amplification for Microbial Single-Cell Genomics. Int J Mol Sci 2023; 24:ijms24054270. [PMID: 36901710 PMCID: PMC10002425 DOI: 10.3390/ijms24054270] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/23/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
Microbial single-cell genomics (SCG) provides access to the genomes of rare and uncultured microorganisms and is a complementary method to metagenomics. Due to the femtogram-levels of DNA in a single microbial cell, sequencing the genome requires whole genome amplification (WGA) as a preliminary step. However, the most common WGA method, multiple displacement amplification (MDA), is known to be costly and biased against specific genomic regions, preventing high-throughput applications and resulting in uneven genome coverage. Thus, obtaining high-quality genomes from many taxa, especially minority members of microbial communities, becomes difficult. Here, we present a volume reduction approach that significantly reduces costs while improving genome coverage and uniformity of DNA amplification products in standard 384-well plates. Our results demonstrate that further volume reduction in specialized and complex setups (e.g., microfluidic chips) is likely unnecessary to obtain higher-quality microbial genomes. This volume reduction method makes SCG more feasible for future studies, thus helping to broaden our knowledge on the diversity and function of understudied and uncharacterized microorganisms in the environment.
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Riojas AM, Spradling-Reeves KD, Christensen CL, Hall-Ursone S, Cox LA. Cell-type deconvolution of bulk RNA-Seq from kidney using opensource bioinformatic tools. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528258. [PMID: 36824792 PMCID: PMC9949078 DOI: 10.1101/2023.02.13.528258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Traditional bulk RNA-Seq pipelines do not assess cell-type composition within heterogeneous tissues. Therefore, it is difficult to determine whether conflicting findings among samples or datasets are the result of biological differences or technical differences due to variation in sample collections. This report provides a user-friendly, open source method to assess cell-type composition in bulk RNA-Seq datasets for heterogeneous tissues using published single cell (sc)RNA-Seq data as a reference. As an example, we apply the method to analysis of kidney cortex bulk RNA-Seq data from female (N=8) and male (N=9) baboons to assess whether observed transcriptome sex differences are biological or technical, i.e., variation due to ultrasound guided biopsy collections. We found cell-type composition was not statistically different in female versus male transcriptomes based on expression of 274 kidney cell-type specific transcripts, indicating differences in gene expression are not due to sampling differences. This method of cell-type composition analysis is recommended for providing rigor in analysis of bulk RNA-Seq datasets from complex tissues. It is clear that with reduced costs, more analyses will be done using scRNA-Seq; however, the approach described here is relevant for data mining and meta analyses of the thousands of bulk RNA-Seq data archived in the NCBI GEO public database.
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Affiliation(s)
- Angelica M. Riojas
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Kimberly D. Spradling-Reeves
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | | | - Shannan Hall-Ursone
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Laura A. Cox
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
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Cao W, Yang Q, Wang QMD. Numerical simulation of vortex flow evolution during droplet formation in T-inlet microchannel. Colloids Surf A Physicochem Eng Asp 2023. [DOI: 10.1016/j.colsurfa.2023.131140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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Jiang Z, Shi H, Tang X, Qin J. Recent advances in droplet microfluidics for single-cell analysis. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Li B, Ma X, Cheng J, Tian T, Guo J, Wang Y, Pang L. Droplets microfluidics platform-A tool for single cell research. Front Bioeng Biotechnol 2023; 11:1121870. [PMID: 37152651 PMCID: PMC10154550 DOI: 10.3389/fbioe.2023.1121870] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/03/2023] [Indexed: 05/09/2023] Open
Abstract
Cells are the most basic structural and functional units of living organisms. Studies of cell growth, differentiation, apoptosis, and cell-cell interactions can help scientists understand the mysteries of living systems. However, there is considerable heterogeneity among cells. Great differences between individuals can be found even within the same cell cluster. Cell heterogeneity can only be clearly expressed and distinguished at the level of single cells. The development of droplet microfluidics technology opens up a new chapter for single-cell analysis. Microfluidic chips can produce many nanoscale monodisperse droplets, which can be used as small isolated micro-laboratories for various high-throughput, precise single-cell analyses. Moreover, gel droplets with good biocompatibility can be used in single-cell cultures and coupled with biomolecules for various downstream analyses of cellular metabolites. The droplets are also maneuverable; through physical and chemical forces, droplets can be divided, fused, and sorted to realize single-cell screening and other related studies. This review describes the channel design, droplet generation, and control technology of droplet microfluidics and gives a detailed overview of the application of droplet microfluidics in single-cell culture, single-cell screening, single-cell detection, and other aspects. Moreover, we provide a recent review of the application of droplet microfluidics in tumor single-cell immunoassays, describe in detail the advantages of microfluidics in tumor research, and predict the development of droplet microfluidics at the single-cell level.
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Affiliation(s)
- Bixuan Li
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
| | - Xi Ma
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
| | - Jianghong Cheng
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
| | - Tian Tian
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
| | - Jiao Guo
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
| | - Yang Wang
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
- *Correspondence: Yang Wang,
| | - Long Pang
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
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Ratnasiri K, Wilk AJ, Lee MJ, Khatri P, Blish CA. Single-cell RNA-seq methods to interrogate virus-host interactions. Semin Immunopathol 2023; 45:71-89. [PMID: 36414692 PMCID: PMC9684776 DOI: 10.1007/s00281-022-00972-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
The twenty-first century has seen the emergence of many epidemic and pandemic viruses, with the most recent being the SARS-CoV-2-driven COVID-19 pandemic. As obligate intracellular parasites, viruses rely on host cells to replicate and produce progeny, resulting in complex virus and host dynamics during an infection. Single-cell RNA sequencing (scRNA-seq), by enabling broad and simultaneous profiling of both host and virus transcripts, represents a powerful technology to unravel the delicate balance between host and virus. In this review, we summarize technological and methodological advances in scRNA-seq and their applications to antiviral immunity. We highlight key scRNA-seq applications that have enabled the understanding of viral genomic and host response heterogeneity, differential responses of infected versus bystander cells, and intercellular communication networks. We expect further development of scRNA-seq technologies and analytical methods, combined with measurements of additional multi-omic modalities and increased availability of publicly accessible scRNA-seq datasets, to enable a better understanding of viral pathogenesis and enhance the development of antiviral therapeutics strategies.
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Affiliation(s)
- Kalani Ratnasiri
- grid.168010.e0000000419368956Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Aaron J. Wilk
- grid.168010.e0000000419368956Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Madeline J. Lee
- grid.168010.e0000000419368956Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Purvesh Khatri
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Department of Medicine, Center for Biomedical Informatics Research, Stanford, CA, USA. .,Inflammatix, Inc., Sunnyvale, CA, 94085, USA.
| | - Catherine A. Blish
- grid.168010.e0000000419368956Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.499295.a0000 0004 9234 0175Chan Zuckerberg Biohub, San Francisco, CA 94158 USA
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Liu M, Zhao D, Lv H, Liang Y, Yang Y, Hong Z, Liu J, Dai K, Xiao X. Controllable Fabrication and Oil-Water Separation Properties of Polyethylene Terephthaloyl-Ethylenediamine-IPN-poly(N-Isopropylacrylamide) Microcapsules. Polymers (Basel) 2022; 15:polym15010053. [PMID: 36616403 PMCID: PMC9824317 DOI: 10.3390/polym15010053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
In this paper, we report a microcapsule embedded PNIPAN in P (TPC-EDA) shell and it can be regarded as an interpenetrating polymer network (IPN) structure, which can accelerate the penetration of oily substances at a certain temperature, and the microcapsules are highly monodisperse and dimensionally reproducible. The proposed microcapsules were fabricated in a three-step process. The first step was the optimization of the conditions for preparing oil in water emulsions by microfluidic device. In the second step, monodisperse polyethylene terephthaloyl-ethylenediamine (P(TPC-EDA)) microcapsules were prepared by interfacial polymerization. In the third step, the final microcapsules with poly(N-isopropylacrylamide) (PNIPAM)-based interpenetrating polymer network (IPN) structure in P(TPC-EDA) shells were finished by free radical polymerization. We conducted careful data analysis on the size of the emulsion prepared by microfluidic technology and used a very intuitive functional relationship to show the production characteristics of microfluidics, which is rarely seen in other literatures. The results show that when the IPN-structured system swelled for 6 h, the adsorption capacity of kerosene was the largest, which was promising for water-oil separation or extraction and separation of hydrophobic drugs. Because we used microfluidic technology, the products obtained have good monodispersity and are expected to be produced in large quantities in industry.
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Affiliation(s)
- Meng Liu
- School of Pharmacy, South-Central University for Nationalities, Wuhan 430074, China
- National Demonstration Center for Experimental Ethnopharmacology Education, South-Central University for Nationalities, Wuhan 430074, China
| | - Dan Zhao
- School of Pharmacy, South-Central University for Nationalities, Wuhan 430074, China
- National Demonstration Center for Experimental Ethnopharmacology Education, South-Central University for Nationalities, Wuhan 430074, China
| | - Hui Lv
- School of Pharmacy, South-Central University for Nationalities, Wuhan 430074, China
- National Demonstration Center for Experimental Ethnopharmacology Education, South-Central University for Nationalities, Wuhan 430074, China
| | - Yunjing Liang
- School of Pharmacy, South-Central University for Nationalities, Wuhan 430074, China
- National Demonstration Center for Experimental Ethnopharmacology Education, South-Central University for Nationalities, Wuhan 430074, China
| | - Yannan Yang
- School of Pharmacy, South-Central University for Nationalities, Wuhan 430074, China
- National Demonstration Center for Experimental Ethnopharmacology Education, South-Central University for Nationalities, Wuhan 430074, China
| | - Zongguo Hong
- School of Pharmacy, South-Central University for Nationalities, Wuhan 430074, China
- National Demonstration Center for Experimental Ethnopharmacology Education, South-Central University for Nationalities, Wuhan 430074, China
| | - Jingxue Liu
- The College of Art and Science, The Ohio State University, Columbus, OH 43210, USA
| | - Kang Dai
- School of Pharmacy, South-Central University for Nationalities, Wuhan 430074, China
- National Demonstration Center for Experimental Ethnopharmacology Education, South-Central University for Nationalities, Wuhan 430074, China
- Correspondence: (K.D.); (X.X.)
| | - Xincai Xiao
- School of Pharmacy, South-Central University for Nationalities, Wuhan 430074, China
- National Demonstration Center for Experimental Ethnopharmacology Education, South-Central University for Nationalities, Wuhan 430074, China
- Correspondence: (K.D.); (X.X.)
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O’Neill H, Lee H, Gupta I, Rodger EJ, Chatterjee A. Single-Cell DNA Methylation Analysis in Cancer. Cancers (Basel) 2022; 14:cancers14246171. [PMID: 36551655 PMCID: PMC9777108 DOI: 10.3390/cancers14246171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/07/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
Morphological, transcriptomic, and genomic defects are well-explored parameters of cancer biology. In more recent years, the impact of epigenetic influences, such as DNA methylation, is becoming more appreciated. Aberrant DNA methylation has been implicated in many types of cancers, influencing cell type, state, transcriptional regulation, and genomic stability to name a few. Traditionally, large populations of cells from the tissue of interest are coalesced for analysis, producing averaged methylome data. Considering the inherent heterogeneity of cancer, analysing populations of cells as a whole denies the ability to discover novel aberrant methylation patterns, identify subpopulations, and trace cell lineages. Due to recent advancements in technology, it is now possible to obtain methylome data from single cells. This has both research and clinical implications, ranging from the identification of biomarkers to improved diagnostic tools. As with all emerging technologies, distinct experimental, bioinformatic, and practical challenges present themselves. This review begins with exploring the potential impact of single-cell sequencing on understanding cancer biology and how it could eventually benefit a clinical setting. Following this, the techniques and experimental approaches which made this technology possible are explored. Finally, the present challenges currently associated with single-cell DNA methylation sequencing are described.
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Affiliation(s)
- Hannah O’Neill
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Heather Lee
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW 2308, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Euan J. Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
- School of Health Sciences and Technology, University of Petroleum and Energy Studies (UPES), Dehradun 248007, India
- Correspondence:
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Recent advances in microfluidic single-cell analysis and its applications in drug development. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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33
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Liu Y, Fan Z, Qiao L, Liu B. Advances in microfluidic strategies for single-cell research. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Ke Y, Jian-yuan H, Ping Z, Yue W, Na X, Jian Y, Kai-xuan L, Yi-fan S, Han-bin L, Rong L. The progressive application of single-cell RNA sequencing technology in cardiovascular diseases. Biomed Pharmacother 2022; 154:113604. [DOI: 10.1016/j.biopha.2022.113604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/02/2022] Open
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Geraldes I, Fernandes M, Fraga AG, Osório NS. The impact of single-cell genomics on the field of mycobacterial infection. Front Microbiol 2022; 13:989464. [PMID: 36246265 PMCID: PMC9562642 DOI: 10.3389/fmicb.2022.989464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/14/2022] [Indexed: 11/13/2022] Open
Abstract
Genome sequencing projects of humans and other organisms reinforced that the complexity of biological systems is largely attributed to the tight regulation of gene expression at the epigenome and RNA levels. As a consequence, plenty of technological developments arose to increase the sequencing resolution to the cell dimension creating the single-cell genomics research field. Single-cell RNA sequencing (scRNA-seq) is leading the advances in this topic and comprises a vast array of different methodologies. scRNA-seq and its variants are more and more used in life science and biomedical research since they provide unbiased transcriptomic sequencing of large populations of individual cells. These methods go beyond the previous “bulk” methodologies and sculpt the biological understanding of cellular heterogeneity and dynamic transcriptomic states of cellular populations in immunology, oncology, and developmental biology fields. Despite the large burden caused by mycobacterial infections, advances in this field obtained via single-cell genomics had been comparatively modest. Nonetheless, seminal research publications using single-cell transcriptomics to study host cells infected by mycobacteria have become recently available. Here, we review these works summarizing the most impactful findings and emphasizing the different and recent single-cell methodologies used, potential issues, and problems. In addition, we aim at providing insights into current research gaps and potential future developments related to the use of single-cell genomics to study mycobacterial infection.
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Affiliation(s)
- Inês Geraldes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's—PT Government Associate Laboratory, Braga, Portugal
| | - Mónica Fernandes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's—PT Government Associate Laboratory, Braga, Portugal
| | - Alexandra G. Fraga
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's—PT Government Associate Laboratory, Braga, Portugal
| | - Nuno S. Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's—PT Government Associate Laboratory, Braga, Portugal
- *Correspondence: Nuno S. Osório
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Habibey R, Rojo Arias JE, Striebel J, Busskamp V. Microfluidics for Neuronal Cell and Circuit Engineering. Chem Rev 2022; 122:14842-14880. [PMID: 36070858 PMCID: PMC9523714 DOI: 10.1021/acs.chemrev.2c00212] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The widespread adoption of microfluidic devices among the neuroscience and neurobiology communities has enabled addressing a broad range of questions at the molecular, cellular, circuit, and system levels. Here, we review biomedical engineering approaches that harness the power of microfluidics for bottom-up generation of neuronal cell types and for the assembly and analysis of neural circuits. Microfluidics-based approaches are instrumental to generate the knowledge necessary for the derivation of diverse neuronal cell types from human pluripotent stem cells, as they enable the isolation and subsequent examination of individual neurons of interest. Moreover, microfluidic devices allow to engineer neural circuits with specific orientations and directionality by providing control over neuronal cell polarity and permitting the isolation of axons in individual microchannels. Similarly, the use of microfluidic chips enables the construction not only of 2D but also of 3D brain, retinal, and peripheral nervous system model circuits. Such brain-on-a-chip and organoid-on-a-chip technologies are promising platforms for studying these organs as they closely recapitulate some aspects of in vivo biological processes. Microfluidic 3D neuronal models, together with 2D in vitro systems, are widely used in many applications ranging from drug development and toxicology studies to neurological disease modeling and personalized medicine. Altogether, microfluidics provide researchers with powerful systems that complement and partially replace animal models.
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Affiliation(s)
- Rouhollah Habibey
- Department of Ophthalmology, Universitäts-Augenklinik Bonn, University of Bonn, Ernst-Abbe-Straße 2, D-53127 Bonn, Germany
| | - Jesús Eduardo Rojo Arias
- Wellcome─MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, United Kingdom
| | - Johannes Striebel
- Department of Ophthalmology, Universitäts-Augenklinik Bonn, University of Bonn, Ernst-Abbe-Straße 2, D-53127 Bonn, Germany
| | - Volker Busskamp
- Department of Ophthalmology, Universitäts-Augenklinik Bonn, University of Bonn, Ernst-Abbe-Straße 2, D-53127 Bonn, Germany
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Liu Y, Chen L, Yu J, Ye L, Hu H, Wang J, Wu B. Advances in Single-Cell Toxicogenomics in Environmental Toxicology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11132-11145. [PMID: 35881918 DOI: 10.1021/acs.est.2c01098] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The toxicity evaluation system of environmental pollutants has undergone numerous changes due to the application of new technologies. Single-cell toxicogenomics is rapidly changing our view on environmental toxicology by increasing the resolution of our analysis to the level of a single cell. Applications of this technology in environmental toxicology have begun to emerge and are rapidly expanding the portfolio of existing technologies and applications. Here, we first summarized different methods involved in single-cell isolation and amplification in single-cell sequencing process, compared the advantages and disadvantages of different methods, and analyzed their development trends. Then, we reviewed the main advances of single-cell toxicogenomics in environmental toxicology, emphatically analyzed the application prospects of this technology in identifying the target cells of pollutants in early embryos, clarifying the heterogeneous response of cell subtypes to pollutants, and finding pathogenic bacteria in unknown microbes, and highlighted the unique characteristics of this approach with high resolution, high throughput, and high specificity by examples. We also offered a prediction of the further application of this technology and the revolution it brings in environmental toxicology. Overall, these advances will provide practical solutions for controlling or mitigating exogenous toxicological effects that threaten human and ecosystem health, contribute to improving our understanding of the physiological processes affected by pollutants, and lead to the emergence of new methods of pollution control.
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Affiliation(s)
- Yuxuan Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Ling Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Jing Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Haidong Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Jinfeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Bing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
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Wang S, Zhou R, Hou Y, Wang M, Hou X. Photochemical effect driven fluid behavior control in microscale pores and channels. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.11.095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Kabay G, Manz A, Dincer C. Microfluidic Roadmap for Translational Nanotheranostics. SMALL METHODS 2022; 6:e2101217. [PMID: 34957704 DOI: 10.1002/smtd.202101217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Nanotheranostic materials (NTMs) shed light on the mechanisms responsible for complex diseases such as cancer because they enable making a diagnosis, monitoring the disease progression, and applying a targeted therapy simultaneously. However, several issues such as the reproducibility and mass production of NTMs hamper their application for clinical practice. To address these issues and facilitate the clinical application of NTMs, microfluidic systems have been increasingly used. This perspective provides a glimpse into the current state-of-art of NTM research, emphasizing the methods currently employed at each development stage of NTMs and the related open problems. This work reviews microfluidic technologies used to develop NTMs, ranging from the fabrication and testing of a single NTM up to their manufacturing on a large scale. Ultimately, a step-by-step vision on the future development of NTMs for clinical practice enabled by microfluidics techniques is provided.
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Affiliation(s)
- Gozde Kabay
- University of Freiburg, Department of Microsystems Engineering (IMTEK), 79110, Freiburg, Germany
- University of Freiburg, FIT Freiburg Center for Interactive Materials and Bioinspired Technologies, 79110, Freiburg, Germany
| | - Andreas Manz
- Korea Institute of Science and Technology (KIST) in Europe, 66123, Saarbrücken, Germany
| | - Can Dincer
- University of Freiburg, Department of Microsystems Engineering (IMTEK), 79110, Freiburg, Germany
- University of Freiburg, FIT Freiburg Center for Interactive Materials and Bioinspired Technologies, 79110, Freiburg, Germany
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Shen F, Shi Y. Recent Advances in Single-Cell View of Mesenchymal Stem Cell in Osteogenesis. Front Cell Dev Biol 2022; 9:809918. [PMID: 35071243 PMCID: PMC8766509 DOI: 10.3389/fcell.2021.809918] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/10/2021] [Indexed: 02/05/2023] Open
Abstract
Osteoblasts continuously replenished by osteoblast progenitor cells form the basis of bone development, maintenance, and regeneration. Mesenchymal stem cells (MSCs) from various tissues can differentiate into the progenitor cell of osteogenic lineage and serve as the main source of osteoblasts. They also respond flexibly to regenerative and anabolic signals emitted by the surrounding microenvironment, thereby maintaining bone homeostasis and participating in bone remodeling. However, MSCs exhibit heterogeneity at multiple levels including different tissue sources and subpopulations which exhibit diversified gene expression and differentiation capacity, and surface markers used to predict cell differentiation potential remain to be further elucidated. The rapid advancement of lineage tracing methods and single-cell technology has made substantial progress in the characterization of osteogenic stem/progenitor cell populations in MSCs. Here, we reviewed the research progress of scRNA-seq technology in the identification of osteogenic markers and differentiation pathways, MSC-related new insights drawn from single-cell technology combined with experimental technology, and recent findings regarding the interaction between stem cell fate and niche in homeostasis and pathological process.
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Affiliation(s)
- Fangyuan Shen
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yu Shi
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Tajabadi M, Goran Orimi H, Ramzgouyan MR, Nemati A, Deravi N, Beheshtizadeh N, Azami M. Regenerative strategies for the consequences of myocardial infarction: Chronological indication and upcoming visions. Biomed Pharmacother 2021; 146:112584. [PMID: 34968921 DOI: 10.1016/j.biopha.2021.112584] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 12/13/2022] Open
Abstract
Heart muscle injury and an elevated troponin level signify myocardial infarction (MI), which may result in defective and uncoordinated segments, reduced cardiac output, and ultimately, death. Physicians apply thrombolytic therapy, coronary artery bypass graft (CABG) surgery, or percutaneous coronary intervention (PCI) to recanalize and restore blood flow to the coronary arteries, albeit they were not convincingly able to solve the heart problems. Thus, researchers aim to introduce novel substitutional therapies for regenerating and functionalizing damaged cardiac tissue based on engineering concepts. Cell-based engineering approaches, utilizing biomaterials, gene, drug, growth factor delivery systems, and tissue engineering are the most leading studies in the field of heart regeneration. Also, understanding the primary cause of MI and thus selecting the most efficient treatment method can be enhanced by preparing microdevices so-called heart-on-a-chip. In this regard, microfluidic approaches can be used as diagnostic platforms or drug screening in cardiac disease treatment. Additionally, bioprinting technique with whole organ 3D printing of human heart with major vessels, cardiomyocytes and endothelial cells can be an ideal goal for cardiac tissue engineering and remarkable achievement in near future. Consequently, this review discusses the different aspects, advancements, and challenges of the mentioned methods with presenting the advantages and disadvantages, chronological indications, and application prospects of various novel therapeutic approaches.
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Affiliation(s)
- Maryam Tajabadi
- School of Metallurgy and Materials Engineering, Iran University of Science and Technology (IUST), Narmak, Tehran 16844, Iran
| | - Hanif Goran Orimi
- School of Metallurgy and Materials Engineering, Iran University of Science and Technology (IUST), Narmak, Tehran 16844, Iran; Regenerative Medicine Group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Maryam Roya Ramzgouyan
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Iran; Regenerative Medicine Group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Alireza Nemati
- Department of Biomedical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran; Regenerative Medicine Group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Niloofar Deravi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Regenerative Medicine Group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Nima Beheshtizadeh
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Iran; Regenerative Medicine Group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Mahmoud Azami
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Iran; Regenerative Medicine Group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
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