Similar Datasets
Project description:Cell states are regulated by extrinsic signals from various external factors such as intercellular interactions, and intrinsic gene expression. Although comprehensive cell state profiling has been attempted, it remains simultaneous analysis of signal activation has still been challenging. Multiplexed imaging is a technique acquiring multiple protein information at a single cell level as traditional immunofluorescence. However, the method often compromises resolution, hindering the analysis of intracellular localization dynamics and post-translational modifications of proteins. To address these limitations, we developed an erasable fluorescence method using disulfide linkers to label antibodies. We term these antibodies ‘Precise Emission Canceling Antibodies (PECAbs)’. PECAb allows for high-resolution iterative imaging with minimal non-specific binding. Automation enables our system to achieve reproducible quantitative analysis using 206 antibodies. The resulting quantitative data allow reconstruction of the spatiotemporal dynamics of signaling pathways over both long and short timescales. Additionally, combining this approach with sequential RNA-FISH can effectively classify cells and identify their signal activation states in human tissue. Overall, the PECAb system serves as a comprehensive platform for analyzing complex cell processes, from signal transduction to gene expression.
2024-04-21 | GSE242886 | GEO
Project description:Cell states are regulated by extrinsic signals from various external factors such as intercellular interactions, and intrinsic gene expression. Although comprehensive cell state profiling has been attempted, it remains simultaneous analysis of signal activation has still been challenging. Multiplexed imaging is a technique acquiring multiple protein information at a single cell level as traditional immunofluorescence. However, the method often compromises resolution, hindering the analysis of intracellular localization dynamics and post-translational modifications of proteins. To address these limitations, we developed an erasable fluorescence method using disulfide linkers to label antibodies. We term these antibodies ‘Precise Emission Canceling Antibodies (PECAbs)’. PECAb allows for high-resolution iterative imaging with minimal non-specific binding. Automation enables our system to achieve reproducible quantitative analysis using 206 antibodies. The resulting quantitative data allow reconstruction of the spatiotemporal dynamics of signaling pathways over both long and short timescales. Additionally, combining this approach with sequential RNA-FISH can effectively classify cells and identify their signal activation states in human tissue. Overall, the PECAb system serves as a comprehensive platform for analyzing complex cell processes, from signal transduction to gene expression.
2024-04-21 | GSE242814 | GEO
Project description:Precise immuno-fluorescence canceling enables highly multiplexed imaging
| PRJNA1015226 | ENA
Project description:Precise immuno-fluorescence canceling enables highly multiplexed imaging [RNA-seq]
| PRJNA1015232 | ENA
Project description:Precise immuno-fluorescence canceling enables highly multiplexed imaging [scRNA-seq]
| PRJNA1014896 | ENA
Project description:Spatial mapping of proteins in tissues is hindered by limitations in multiplexing, sensitivity and throughput. Here we report immunostaining with signal amplification by exchange reaction (Immuno-SABER), which achieves highly multiplexed signal amplification via DNA-barcoded antibodies and orthogonal DNA concatemers generated by primer exchange reaction (PER). SABER offers independently programmable signal amplification without in situ enzymatic reactions, and intrinsic scalability to rapidly amplify and visualize a large number of targets when combined with fast exchange cycles of fluorescent imager strands. We demonstrate 5- to 180-fold signal amplification in diverse samples (cultured cells, cryosections, formalin-fixed paraffin-embedded sections and whole-mount tissues), as well as simultaneous signal amplification for ten different proteins using standard equipment and workflows. We also combined SABER with expansion microscopy to enable rapid, multiplexed super-resolution tissue imaging. Immuno-SABER presents an effective and accessible platform for multiplexed and amplified imaging of proteins with high sensitivity and throughput.
| S-EPMC6728175 | biostudies-literature
Project description:The multiplexing capability of fluorescence microscopy is severely limited by the broad fluorescence spectral width. Spectral imaging offers potential solutions, yet typical approaches to disperse the local emission spectra notably impede the attainable throughput. Here we show that using a single, fixed fluorescence emission detection band, through frame-synchronized fast scanning of the excitation wavelength from a white lamp via an acousto-optic tunable filter, up to six subcellular targets, labeled by common fluorophores of substantial spectral overlap, can be simultaneously imaged in live cells with low (~1%) crosstalks and high temporal resolutions (down to ~10 ms). The demonstrated capability to quantify the abundances of different fluorophores in the same sample through unmixing the excitation spectra next enables us to devise novel, quantitative imaging schemes for both bi-state and Förster resonance energy transfer fluorescent biosensors in live cells. We thus achieve high sensitivities and spatiotemporal resolutions in quantifying the mitochondrial matrix pH and intracellular macromolecular crowding, and further demonstrate, for the first time, the multiplexing of absolute pH imaging with three additional target organelles/proteins to elucidate the complex, Parkin-mediated mitophagy pathway. Together, excitation spectral microscopy provides exceptional opportunities for highly multiplexed fluorescence imaging. The prospect of acquiring fast spectral images without the need for fluorescence dispersion or care for the spectral response of the detector offers tremendous potential.
| S-EPMC8105378 | biostudies-literature
Project description:The excited-state lifetime is an intrinsic property of fluorescent molecules that can be leveraged for multiplexed imaging. An advantage of fluorescence lifetime-based multiplexing is that signals from multiple probes can be gathered simultaneously, whereas traditional spectral fluorescence imaging typically requires multiple images at different excitation and emission wavelengths. Additionally, lifetime and spectra could both be utilized to expand the multiplexing capacity of fluorescence. However, resolving exogenous molecular probes based exclusively on the fluorescence lifetime has been limited by technical challenges in analyzing lifetime data. The phasor approach to lifetime analysis offers a simple, graphical solution that has increasingly been used to assess endogenous cellular autofluorescence to quantify metabolic factors. In this study, we employed the phasor analysis of FLIM to quantitatively resolve three exogenous, antibody-targeted fluorescent probes with similar spectral properties based on lifetime information alone. First, we demonstrated that three biomarkers that were spatially restricted to the cell membrane, cytosol, or nucleus could be accurately distinguished using FLIM and phasor analysis. Next, we successfully resolved and quantified three probes that were all targeted to cell surface biomarkers. Finally, we demonstrated that lifetime-based quantitation accuracy can be improved through intensity matching of various probe-biomarker combinations, which will expand the utility of this technique. Importantly, we reconstructed images for each individual probe, as well as an overlay of all three probes, from a single FLIM image. Our results demonstrate that FLIM and phasor analysis can be leveraged as a powerful tool for simultaneous detection of multiple biomarkers with high sensitivity and accuracy.
| S-EPMC10681155 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2023-02-01 | GSE206425 | GEO
Project description:Antibody-based dual-modality (PET/fluorescence) imaging enables both presurgery antigen-specific immuno-PET for noninvasive whole-body evaluation and intraoperative fluorescence for visualization of superficial tissue layers for image-guided surgery. Methods: We developed a universal dual-modality linker (DML) that facilitates site-specific conjugation to a cysteine residue-bearing antibody fragment, introduction of a commercially available fluorescent dye (via an amine-reactive prosthetic group), and rapid and efficient radiolabeling via click chemistry with 18F-labeled trans-cyclooctene (18F-TCO). To generate a dual-modality antibody fragment-based imaging agent, the DML was labeled with the far-red dye sulfonate cyanine 5 (sCy5), site-specifically conjugated to the C-terminal cysteine of the anti-prostate stem cell antigen (PSCA) cys-diabody A2, and subsequently radiolabeled by click chemistry with 18F-TCO. The new imaging probe was evaluated in a human PSCA-positive prostate cancer xenograft model by sequential immuno-PET and optical imaging. Uptake in target tissues was confirmed by ex vivo biodistribution. Results: We successfully synthesized a DML for conjugation of a fluorescent dye and 18F. The anti-PSCA cys-diabody A2 was site-specifically conjugated with either DML or sCy5 and radiolabeled via click chemistry with 18F-TCO. Immuno-PET imaging confirmed in vivo antigen-specific targeting of prostate cancer xenografts as early as 1 h after injection. Rapid renal clearance of the 50-kDa antibody fragment enables same-day imaging. Optical imaging showed antigen-specific fluorescent signal in PSCA-positive xenografts and high contrast to surrounding tissue and PSCA-negative xenografts. Conclusion: The DML enables site-specific conjugation away from the antigen-binding site of antibody fragments, with a controlled linker-to-protein ratio, and combines signaling moieties for 2 imaging systems into 1 molecule. Dual-modality imaging could provide both noninvasive whole-body imaging with organ-level biodistribution and fluorescence image-guided identification of tumor margins during surgery.
| S-EPMC6785789 | biostudies-literature