Spatially resolved proteomics via tissue expansion

Li, Lü; Sun, Cuiji; Sun, Yaoting; Dong, Zhen; Wu, Runxin; Sun, Xiaorui; Zhang, Hanbin; Jiang, Wenhao; Zhou, Yan; Cen, Xufeng; Cai, Shanbao; Xia, Hong; Zhu, Yi; Guo, Tiannan; Piatkevich, Kiryl D.

doi:10.1038/s41467-022-34824-2

Cited by 26 publications

(27 citation statements)

References 51 publications

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“…Protocols have been developed that enable both DNA (Klimas et al, 2023) and RNA (Chen et al, 2016) FISH on expanded samples, opening the possibility of studying individual genomic loci or RNAs on expanded parasites. Omics technologies have also recently been combined with expansion microscopy, with protocols recently published to perform in situ spatial transcriptomics (Alon et al, 2021) and proteomics (Li, Sun, et al, 2022) on expanded samples. These techniques are not yet at the level of single‐cell transcriptomics or proteomics, but we can image this kind of technique being applied to decipher a single‐cell transcriptome or proteome of something like the P. vivax hypnozoite.…”

Section: Potential Future Applications and Emerging Expansion Microsc...mentioning

confidence: 99%

Expansion microscopy of apicomplexan parasites

Liffner

Absalon

2023

Molecular Microbiology

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Apicomplexan parasites comprise significant pathogens of humans, livestock and wildlife, but also represent a diverse group of eukaryotes with interesting and unique cell biology. The study of cell biology in apicomplexan parasites is complicated by their small size, and historically this has required the application of cutting‐edge microscopy techniques to investigate fundamental processes like mitosis or cell division in these organisms. Recently, a technique called expansion microscopy has been developed, which rather than increasing instrument resolution like most imaging modalities, physically expands a biological sample. In only a few years since its development, a derivative of expansion microscopy known as ultrastructure‐expansion microscopy (U‐ExM) has been widely adopted and proven extremely useful for studying cell biology of Apicomplexa. Here, we review the insights into apicomplexan cell biology that have been enabled through the use of U‐ExM, with a specific focus on Plasmodium, Toxoplasma and Cryptosporidium. Further, we summarize emerging expansion microscopy modifications and modalities and forecast how these may influence the field of parasite cell biology in future.

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Section: Potential Future Applications and Emerging Expansion Microsc...mentioning

confidence: 99%

Expansion microscopy of apicomplexan parasites

Liffner

Absalon

2023

Molecular Microbiology

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“…Light sheet microscopy has also been combined with ExM to largely increase the speed of image acquisition in expanded samples, making it easier for the 3D reconstruction of large-volume samples such as expanded tissues. , In addition, tissue expansion is also compatible with mass spectrometry-based spatial proteomic analysis. For example, it was demonstrated, using manual microdissection, that proteomics profiling of tissues can be assessed at ∼330 μm lateral resolution in mass spectrometry imaging when using a 3-fold expansion factor in the linear dimension and a higher lateral resolution of ∼160 μm can be achieved when expanding samples 8-fold …”

Section: Exm Combined With Diffraction Unlimited Imaging Methodsmentioning

confidence: 99%

“…For example, it was demonstrated, using manual microdissection, that proteomics profiling of tissues can be assessed at ∼330 μm lateral resolution in mass spectrometry imaging when using a 3-fold expansion factor in the linear dimension 80 and a higher lateral resolution of ∼160 μm can be achieved when expanding samples 8-fold. 81…”

Section: Exm Combined With Diffraction Unlimited Imaging Methodsmentioning

confidence: 99%

Current Progress in Expansion Microscopy: Chemical Strategies and Applications

Wen

Leen²,

Rohand

et al. 2023

Chem. Rev.

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Expansion microscopy (ExM) is a newly developed super-resolution technique, allowing visualization of biological targets at nanoscale resolution on conventional fluorescence microscopes. Since its introduction in 2015, many efforts have been dedicated to broaden its application range or increase the resolution that can be achieved. As a consequence, recent years have witnessed remarkable advances in ExM. This review summarizes recent progress in ExM, with the focus on the chemical aspects of the method, from chemistries for biomolecule grafting to polymer synthesis and the impact on biological analysis. The combination of ExM with other microscopy techniques, in search of additional resolution improvement, is also discussed. In addition, we compare pre-and postexpansion labeling strategies and discuss the impact of fixation methods on ultrastructure preservation. We conclude this review with a perspective on existing challenges and future directions. We believe that this review will provide a comprehensive understanding of ExM and facilitate its usage and further development. CONTENTS R 8. Expansion Isotropy S 9. Conclusion and Outlook S

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“…Expansion microscopy is one example of this technique, and it was the first and most widely known to use this approach. [ 14 ] Together, other techniques have since been developed based on this approach, such as exTEM, [ 15 ] spatially resolved proteomics, [ 16 ] expansion sequencing, [ 17 ] to name but a few.…”

Section: Introductionmentioning

confidence: 99%

Signal Amplification by Spatial Concentration for Immunoassay on Cellulose Media

Kim,

Noh

2023

Small

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Immunoassay is one of the most common bioanalytical techniques from lab‐based to point‐of‐care settings. Over time, various approaches have been developed to amplify signals for greater sensitivity. However, the need for effective, versatile, and simple signal amplification methods persists yet. This paper presents a novel signal amplification method for immunoassay that utilizes spatial concentration of a cellulose‐based plate possessing sensor transducers, specifically gold nanoparticles. By modifying the dimensions of the plate, the density of nanoparticles increased, resulting in intensified color signals. The coating material, polydopamine, which is utilized to protect the gold nanoparticles. Chemical changes in nanocomposites are characterized using scanning electron microscopy, Raman spectroscopy, Fourier transform infrared spectroscopy, X‐ray photoelectron spectroscopy, and scanning electron microscopy. The application of this method to colorimetric quantification demonstrated great consistency across various concentrations of nanoparticles, with better reliability at lower concentration ranges. A model immunoassay is designed to evaluate the analytical performance. As a result, this method successfully corrected a false‐negative result with a lowered Kd of 0.509 pmol per zone. This method shows strong signal enhancement capability that can correct false‐negative signals in the immunoassays, with potential benefits including versatility, simplicity, low cost, and the ability to operate multiple plates simultaneously.

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Spatially resolved proteomics via tissue expansion

Cited by 26 publications

References 51 publications

Expansion microscopy of apicomplexan parasites

Expansion microscopy of apicomplexan parasites

Current Progress in Expansion Microscopy: Chemical Strategies and Applications

Signal Amplification by Spatial Concentration for Immunoassay on Cellulose Media

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