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Pham DL, Gillette AA, Riendeau J, Wiech K, Guzman EC, Datta R, Skala MC. Perspectives on label-free microscopy of heterogeneous and dynamic biological systems. JOURNAL OF BIOMEDICAL OPTICS 2025; 29:S22702. [PMID: 38434231 PMCID: PMC10903072 DOI: 10.1117/1.jbo.29.s2.s22702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/22/2023] [Accepted: 12/14/2023] [Indexed: 03/05/2024]
Abstract
Significance Advancements in label-free microscopy could provide real-time, non-invasive imaging with unique sources of contrast and automated standardized analysis to characterize heterogeneous and dynamic biological processes. These tools would overcome challenges with widely used methods that are destructive (e.g., histology, flow cytometry) or lack cellular resolution (e.g., plate-based assays, whole animal bioluminescence imaging). Aim This perspective aims to (1) justify the need for label-free microscopy to track heterogeneous cellular functions over time and space within unperturbed systems and (2) recommend improvements regarding instrumentation, image analysis, and image interpretation to address these needs. Approach Three key research areas (cancer research, autoimmune disease, and tissue and cell engineering) are considered to support the need for label-free microscopy to characterize heterogeneity and dynamics within biological systems. Based on the strengths (e.g., multiple sources of molecular contrast, non-invasive monitoring) and weaknesses (e.g., imaging depth, image interpretation) of several label-free microscopy modalities, improvements for future imaging systems are recommended. Conclusion Improvements in instrumentation including strategies that increase resolution and imaging speed, standardization and centralization of image analysis tools, and robust data validation and interpretation will expand the applications of label-free microscopy to study heterogeneous and dynamic biological systems.
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Affiliation(s)
- Dan L. Pham
- University of Wisconsin—Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
| | | | | | - Kasia Wiech
- University of Wisconsin—Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
| | | | - Rupsa Datta
- Morgridge Institute for Research, Madison, Wisconsin, United States
| | - Melissa C. Skala
- University of Wisconsin—Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
- Morgridge Institute for Research, Madison, Wisconsin, United States
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2
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Lu S, Huang Y, Shen WX, Cao YL, Cai M, Chen Y, Tan Y, Jiang YY, Chen YZ. Raman spectroscopic deep learning with signal aggregated representations for enhanced cell phenotype and signature identification. PNAS NEXUS 2024; 3:pgae268. [PMID: 39192845 PMCID: PMC11348106 DOI: 10.1093/pnasnexus/pgae268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 06/21/2024] [Indexed: 08/29/2024]
Abstract
Feature representation is critical for data learning, particularly in learning spectroscopic data. Machine learning (ML) and deep learning (DL) models learn Raman spectra for rapid, nondestructive, and label-free cell phenotype identification, which facilitate diagnostic, therapeutic, forensic, and microbiological applications. But these are challenged by high-dimensional, unordered, and low-sample spectroscopic data. Here, we introduced novel 2D image-like dual signal and component aggregated representations by restructuring Raman spectra and principal components, which enables spectroscopic DL for enhanced cell phenotype and signature identification. New ConvNet models DSCARNets significantly outperformed the state-of-the-art (SOTA) ML and DL models on six benchmark datasets, mostly with >2% improvement over the SOTA performance of 85-97% accuracies. DSCARNets also performed well on four additional datasets against SOTA models of extremely high performances (>98%) and two datasets without a published supervised phenotype classification model. Explainable DSCARNets identified Raman signatures consistent with experimental indications.
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Affiliation(s)
- Songlin Lu
- The State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, 2279 Lishui Road, Nanshan District, Shenzhen 518055, Guangdong, P. R. China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, 9 Kexue Avenue, Guangming District, Shenzhen 518132, Guangdong, P. R. China
| | - Yuanfang Huang
- The State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, 2279 Lishui Road, Nanshan District, Shenzhen 518055, Guangdong, P. R. China
| | - Wan Xiang Shen
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore
| | - Yu Lin Cao
- Tangyi and Tsinghua Shenzhen International Graduate School Collaborative Program, Tsinghua University, 2279 Lishui Road, Nanshan District, Shenzhen 518055, Guangdong, P. R. China
| | - Mengna Cai
- Tangyi and Tsinghua Shenzhen International Graduate School Collaborative Program, Tsinghua University, 2279 Lishui Road, Nanshan District, Shenzhen 518055, Guangdong, P. R. China
| | - Yan Chen
- The State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, 2279 Lishui Road, Nanshan District, Shenzhen 518055, Guangdong, P. R. China
- Shenzhen Kivita Innovative Drug Discovery Institute, Shenzhen 518057, Guangdong, P. R. China
| | - Ying Tan
- The State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, 2279 Lishui Road, Nanshan District, Shenzhen 518055, Guangdong, P. R. China
- Institute of Drug Discovery Technology, Ningbo University, 818 Fenghua Road, Ningbo 315211, Zhejiang, P. R. China
| | - Yu Yang Jiang
- School of Pharmaceutical Sciences, Tsinghua University, 30 Shuangqing Road, Haidian District, Beijing 100084, P. R. China
| | - Yu Zong Chen
- The State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, 2279 Lishui Road, Nanshan District, Shenzhen 518055, Guangdong, P. R. China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, 9 Kexue Avenue, Guangming District, Shenzhen 518132, Guangdong, P. R. China
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3
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Akagi Y, Norimoto A, Kawamura T, Kida YS. Label-Free Assessment of Neuronal Activity Using Raman Micro-Spectroscopy. Molecules 2024; 29:3174. [PMID: 38999126 PMCID: PMC11243074 DOI: 10.3390/molecules29133174] [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: 06/12/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/14/2024] Open
Abstract
Given the pivotal role of neuronal populations in various biological processes, assessing their collective output is crucial for understanding the nervous system's complex functions. Building on our prior development of a spiral scanning mechanism for the rapid acquisition of Raman spectra from single cells and incorporating machine learning for label-free evaluation of cell states, we investigated whether the Paint Raman Express Spectroscopy System (PRESS) can assess neuronal activities. We tested this hypothesis by examining the chemical responses of glutamatergic neurons as individual neurons and autonomic neuron ganglia as neuronal populations derived from human-induced pluripotent stem cells. The PRESS successfully acquired Raman spectra from both individual neurons and ganglia within a few seconds, achieving a signal-to-noise ratio sufficient for detailed analysis. To evaluate the ligand responsiveness of the induced neurons and ganglia, the Raman spectra were subjected to principal component and partial least squares discriminant analyses. The PRESS detected neuronal activity in response to glutamate and nicotine, which were absent in the absence of calcium. Additionally, the PRESS induced dose-dependent neuronal activity changes. These findings underscore the capability of the PRESS to assess individual neuronal activity and elucidate neuronal population dynamics and pharmacological responses, heralding new opportunities for drug discovery and regenerative medicine advancement.
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Affiliation(s)
- Yuka Akagi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba 305-8565, Ibaraki, Japan; (Y.A.); (A.N.)
| | - Aya Norimoto
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba 305-8565, Ibaraki, Japan; (Y.A.); (A.N.)
| | - Teruhisa Kawamura
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu 525-8577, Shiga, Japan;
| | - Yasuyuki S. Kida
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba 305-8565, Ibaraki, Japan; (Y.A.); (A.N.)
- School of Integrative & Global Majors, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8572, Ibaraki, Japan
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4
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Nikolaev VV, Kistenev YV, Kröger M, Zuhayri H, Darvin ME. Review of optical methods for noninvasive imaging of skin fibroblasts-From in vitro to ex vivo and in vivo visualization. JOURNAL OF BIOPHOTONICS 2024; 17:e202300223. [PMID: 38018868 DOI: 10.1002/jbio.202300223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/21/2023] [Accepted: 10/25/2023] [Indexed: 11/30/2023]
Abstract
Fibroblasts are among the most common cell types in the stroma responsible for creating and maintaining the structural organization of the extracellular matrix in the dermis, skin regeneration, and a range of immune responses. Until now, the processes of fibroblast adaptation and functioning in a varying environment have not been fully understood. Modern laser microscopes are capable of studying fibroblasts in vitro and ex vivo. One-photon- and two-photon-excited fluorescence microscopy, Raman spectroscopy/microspectroscopy are well-suited noninvasive optical methods for fibroblast imaging in vitro and ex vivo. In vivo staining-free fibroblast imaging is not still implemented. The exception is fibroblast imaging in tattooed skin. Although in vivo noninvasive staining-free imaging of fibroblasts in the skin has not yet been implemented, it is expected in the future. This review summarizes the state-of-the-art in fibroblast visualization using optical methods and discusses the advantages, limitations, and prospects for future noninvasive imaging.
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Affiliation(s)
- Viktor V Nikolaev
- Tomsk State University, Laboratory of Molecular Imaging and Machine Learning, Tomsk, Russia
| | - Yury V Kistenev
- Tomsk State University, Laboratory of Molecular Imaging and Machine Learning, Tomsk, Russia
| | - Marius Kröger
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Dermatology, Venerology and Allergology, Center of Experimental and Applied Cutaneous Physiology, Berlin, Germany
| | - Hala Zuhayri
- Tomsk State University, Laboratory of Molecular Imaging and Machine Learning, Tomsk, Russia
| | - Maxim E Darvin
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Dermatology, Venerology and Allergology, Center of Experimental and Applied Cutaneous Physiology, Berlin, Germany
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5
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Oshima Y, Haruki T, Koizumi K, Yonezawa S, Taketani A, Kadowaki M, Saito S. Practices, Potential, and Perspectives for Detecting Predisease Using Raman Spectroscopy. Int J Mol Sci 2023; 24:12170. [PMID: 37569541 PMCID: PMC10418989 DOI: 10.3390/ijms241512170] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/23/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Raman spectroscopy shows great potential for practical clinical applications. By analyzing the structure and composition of molecules through real-time, non-destructive measurements of the scattered light from living cells and tissues, it offers valuable insights. The Raman spectral data directly link to the molecular composition of the cells and tissues and provides a "molecular fingerprint" for various disease states. This review focuses on the practical and clinical applications of Raman spectroscopy, especially in the early detection of human diseases. Identifying predisease, which marks the transition from a healthy to a disease state, is crucial for effective interventions to prevent disease onset. Raman spectroscopy can reveal biological processes occurring during the transition states and may eventually detect the molecular dynamics in predisease conditions.
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Affiliation(s)
- Yusuke Oshima
- Faculty of Engineering, University of Toyama, Toyama 930-8555, Japan
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
- Faculty of Medicine, Oita University, Yufu 879-5593, Japan
| | - Takayuki Haruki
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
- Faculty of Sustainable Design, University of Toyama, Toyama 930-8555, Japan
| | - Keiichi Koizumi
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
- Division of Presymptomatic Disease, Institute of Natural Medicine, University of Toyama, Toyama 930-8555, Japan
| | - Shota Yonezawa
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Akinori Taketani
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Makoto Kadowaki
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
| | - Shigeru Saito
- Research Center for Pre-Disease Science, University of Toyama, Toyama 930-8555, Japan
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6
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Cutshaw G, Uthaman S, Hassan N, Kothadiya S, Wen X, Bardhan R. The Emerging Role of Raman Spectroscopy as an Omics Approach for Metabolic Profiling and Biomarker Detection toward Precision Medicine. Chem Rev 2023; 123:8297-8346. [PMID: 37318957 PMCID: PMC10626597 DOI: 10.1021/acs.chemrev.2c00897] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Omics technologies have rapidly evolved with the unprecedented potential to shape precision medicine. Novel omics approaches are imperative toallow rapid and accurate data collection and integration with clinical information and enable a new era of healthcare. In this comprehensive review, we highlight the utility of Raman spectroscopy (RS) as an emerging omics technology for clinically relevant applications using clinically significant samples and models. We discuss the use of RS both as a label-free approach for probing the intrinsic metabolites of biological materials, and as a labeled approach where signal from Raman reporters conjugated to nanoparticles (NPs) serve as an indirect measure for tracking protein biomarkers in vivo and for high throughout proteomics. We summarize the use of machine learning algorithms for processing RS data to allow accurate detection and evaluation of treatment response specifically focusing on cancer, cardiac, gastrointestinal, and neurodegenerative diseases. We also highlight the integration of RS with established omics approaches for holistic diagnostic information. Further, we elaborate on metal-free NPs that leverage the biological Raman-silent region overcoming the challenges of traditional metal NPs. We conclude the review with an outlook on future directions that will ultimately allow the adaptation of RS as a clinical approach and revolutionize precision medicine.
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Affiliation(s)
- Gabriel Cutshaw
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50012, USA
- Nanovaccine Institute, Iowa State University, Ames, IA 50012, USA
| | - Saji Uthaman
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50012, USA
- Nanovaccine Institute, Iowa State University, Ames, IA 50012, USA
| | - Nora Hassan
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50012, USA
- Nanovaccine Institute, Iowa State University, Ames, IA 50012, USA
| | - Siddhant Kothadiya
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50012, USA
- Nanovaccine Institute, Iowa State University, Ames, IA 50012, USA
| | - Xiaona Wen
- Biologics Analytical Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Rizia Bardhan
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50012, USA
- Nanovaccine Institute, Iowa State University, Ames, IA 50012, USA
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7
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Pavillon N, Smith NI. Non-invasive monitoring of T cell differentiation through Raman spectroscopy. Sci Rep 2023; 13:3129. [PMID: 36813799 PMCID: PMC9947172 DOI: 10.1038/s41598-023-29259-8] [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: 12/17/2022] [Accepted: 02/01/2023] [Indexed: 02/24/2023] Open
Abstract
The monitoring of dynamic cellular behaviors remains a technical challenge for most established techniques used nowadays for single-cell analysis, as most of them are either destructive, or rely on labels that can affect the long-term functions of cells. We employ here label-free optical techniques to non-invasively monitor the changes that occur in murine naive T cells upon activation and subsequent differentiation into effector cells. Based on spontaneous Raman single-cell spectra, we develop statistical models that allow the detection of activation, and employ non-linear projection methods to delineate the changes occurring over a several day period spanning early differentiation. We show that these label-free results have very high correlation with known surface markers of activation and differentiation, while also providing spectral models that allow the identification of the underlying molecular species that are representative of the biological process under study.
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Affiliation(s)
- Nicolas Pavillon
- Biophotonics Laboratory, Immunology Frontier Research Center (IFReC), Osaka University, Yamadaoka 3-1, Suita, Osaka, 565-0871, Japan.
| | - Nicholas I. Smith
- grid.136593.b0000 0004 0373 3971Biophotonics Laboratory, Immunology Frontier Research Center (IFReC), Osaka University, Yamadaoka 3-1, Suita, Osaka 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Open and Transdisciplinary Research Institute (OTRI), Osaka University, Yamadaoka 3-1, Suita, Osaka 565-0871 Japan
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8
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Microscopic image-based classification of adipocyte differentiation by machine learning. Histochem Cell Biol 2022; 159:313-327. [PMID: 36504003 DOI: 10.1007/s00418-022-02168-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
Adipocyte differentiation is a sequential process involving increased expression of peroxisome proliferator-activated receptor gamma (PPARγ), adipocyte-specific gene expression, and accumulation of lipid droplets in the cytoplasm. Expression of the transcription factors involved is usually detected using canonical biochemical or biomolecular procedures such as Western blotting or qPCR of pooled cell lysates. While this provides a useful average index for adipogenesis for some populations, the precise stage of adipogenesis cannot be distinguished at the single-cell level, because the heterogenous nature of differentiation among cells limits the utility of averaged data. We have created a classifier to sort cells, and used it to determine the stage of adipocyte differentiation at the single-cell level. We used a machine learning method with microscopic images of cell stained for PPARγ and lipid droplets as input data. Our results show that the classifier can successfully determine the precise stage of differentiation. Stage classification and subsequent model fitting using the sequential reaction model revealed the action of pioglitazone and rosiglitazone to be promotion of transition from the stage of increased PPARγ expression to the next stage. This indicates that these drugs are PPARγ agonists, and that our classifier and model can accurately estimate drug action points and would be suitable for evaluating the stage/state of individual cells during differentiation or disease progression. The incorporation of both biochemical and morphological information derived from immunofluorescence image of cells and so overcomes limitations of current models.
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Particles in Biopharmaceutical Formulations, Part 2: An Update on Analytical Techniques and Applications for Therapeutic Proteins, Viruses, Vaccines and Cells. J Pharm Sci 2021; 111:933-950. [PMID: 34919969 DOI: 10.1016/j.xphs.2021.12.011] [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: 12/07/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 11/21/2022]
Abstract
Particles in biopharmaceutical formulations remain a hot topic in drug product development. With new product classes emerging it is crucial to discriminate particulate active pharmaceutical ingredients from particulate impurities. Technical improvements, new analytical developments and emerging tools (e.g., machine learning tools) increase the amount of information generated for particles. For a proper interpretation and judgment of the generated data a thorough understanding of the measurement principle, suitable application fields and potential limitations and pitfalls is required. Our review provides a comprehensive overview of novel particle analysis techniques emerging in the last decade for particulate impurities in therapeutic protein formulations (protein-related, excipient-related and primary packaging material-related), as well as particulate biopharmaceutical formulations (virus particles, virus-like particles, lipid nanoparticles and cell-based medicinal products). In addition, we review the literature on applications, describe specific analytical approaches and illustrate advantages and drawbacks of currently available techniques for particulate biopharmaceutical formulations.
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