Quantifying single-cell secretion in real time using resonant hyperspectral imaging

Multimodal Nanoplasmonic and Fluorescence Imaging for Simultaneous Monitoring of Single-Cell Secretory and Intracellular Dynamics

Current imaging technologies are limited in their capability to simultaneously capture intracellular and extracellular dynamics in a spatially and temporally resolved manner. This study presents a multimodal imaging system that integrates nanoplasmonic sensing with multichannel fluorescence imaging to concomitantly analyze intracellular and extracellular processes in space and time at the single-cell level. Utilizing a highly sensitive gold nanohole array biosensor, the system provides label-free and real-time monitoring of extracellular secretion, while implementing nanoplasmonic-compatible multichannel fluorescence microscopy enables to visualize the interconnected intracellular activities. Combined with deep-learning-assisted image processing, this integrated approach allows multiparametric and simultaneous study of various cellular constituents in hundreds of individual cells with subcellular spatial and minute-level temporal resolution over extended periods of up to 20 h. The system's utility is demonstrated by characterizing a range of secreted biomolecules and fluorescence toolkits across three distinct applications: visualization of secretory behaviors along with subcellular organelles and metabolic processes, concurrent monitoring of protein expression and secretion, and assessment of cell cycle phases alongside their corresponding secretory profiles. By offering comprehensive insights, the multifunctional approach is expected to enhance holistic readouts of biological systems, facilitating new discoveries in both fundamental and translational sciences.

Time-resolved single-cell secretion analysis via microfluidics

Revealing how individual cells alter their secretions over time is crucial for understanding their responses to environmental changes. Key questions include: When do cells modify their functions and states? What transitions occur? Insights into the kinetic secretion trajectories of various cell types are essential for unraveling complex biological systems. This review highlights seven microfluidic technologies for time-resolved single-cell secretion analysis: 1. Microwell real-time electrical detection: uses microelectrodes for precise, cell-specific, real-time measurement of secreted molecules. 2. Microwell real-time optical detection: employs advanced optical systems for real-time, multiplexed monitoring of cellular secretions. 3. Microvalve real-time optical detection: dynamically analyzes secretions under controlled in situ stimuli, enabling detailed kinetic studies at the single-cell level. 4. Droplet real-time optical detection: provides superior throughput by generating droplets containing single cells and sensors for high-throughput screening. 5. Microwell time-barcoded optical detection: utilizes sequential barcoding techniques to facilitate scalable assays for tracking multiple secretions over time. 6. Microvalve time-barcoded optical detection: incorporates automated time-barcoding via micro-valves for robust and scalable analysis. 7. Microwell time-barcoded sequencing: captures and labels secretions for sequencing, enabling multidimensional analysis, though currently limited to a few time points and extended intervals. This review specifically addresses the challenges of achieving high-resolution timing measurements with short intervals while maintaining scalability for single-cell screening. Future advancements in microfluidic devices, integrating innovative barcoding technologies, advanced imaging technologies, artificial intelligence-powered decoding and analysis, and automations are anticipated to enable highly sensitive, scalable, high-throughput single-cell dynamic analysis. These developments hold great promise for deepening our understanding of biosystems by exploring single-cell timing responses on a larger scale.

Bio-inspired polydopamine layer as a versatile functionalisation protocol for silicon-based photonic biosensors

Photonic biosensors have made major advances in recent years, achieving very high sensitivity, and progressing towards point-of-care deployment. By using photonic resonances, sensors can be label-free, which is particularly attractive for a low-cost technological realisation. A key remaining issue is the biological interface and the efficient and reliable immobilisation of binder molecules such as antibodies; many protocols are currently in use that have led to widely varying sensor performance. Here, we study a very simple and robust surface functionalisation protocol for silicon photonics, which is based on polydopamine, and we demonstrate both its simplicity and its high performance. The use of polydopamine (PDA) is inspired by molluscs, especially mussels, that employ dopamine to adhere to virtually any surface, especially in an aqueous environment. We studied the versatility of the PDA protocol by showing compatibility with 5 different disease biomarkers (Immunoglobulin (IgG), C-reactive protein (CRP), Tumour Necrosis factor-α (TNF-α), Interleukin-6 (IL-6), Matrix metalloproteinase (MMP-9) and show that the protocol is resistant to hydrolysis during incubation; the loss of functionality due to hydrolysis is a major issue for many of the functionalisation protocols commonly used for silicon-based sensors. The study using guided mode resonance-based sensors highlights the wide dynamic range of the protocol (0.01 ng/mL to 1 μg/mL), using IgG, CRP and MMP-9 protein biomarkers as exemplars. In addition, we show that the surface chemistry allows performing measurements in 10% human serum with a sensitivity as low as 10 ng/mL for IgG. We suggest that adopting this protocol will make it easier for researchers to achieve biofunctionalisation and that the biosensor community will be able to achieve more consistent results.

Real-Time Spatiotemporal Measurement of Extracellular Signaling Molecules Using an Aptamer Switch-Conjugated Hydrogel Matrix

Cells rely on secreted signaling molecules to coordinate essential biological functions including development, metabolism, and immunity. Unfortunately, such signaling processes remain difficult to measure with sufficient chemical specificity and temporal resolution. To address this need, an aptamer-conjugated hydrogel matrix that enables continuous fluorescent measurement of specific secreted analytes - in two dimensions, in real-time is developed. As a proof of concept, real-time imaging of inter-cellular cyclic adenosine 3',5'-monophosphate (cAMP) signals in Dictyostelium discoideum amoeba cells is performed. A set of aptamer switches that generate a rapid and reversible change in fluorescence in response to cAMP signals is engineered. By combining multiple switches with different dynamic ranges, measure cAMP concentrations spanning three orders of magnitude in a single experiment can be measured. These sensors are embedded within a biocompatible hydrogel on which cells are cultured and their cAMP secretions can be imaged using fluorescent microscopy. Using this aptamer-hydrogel material system, the first direct measurements of oscillatory cAMP signaling that correlate closely with previous indirect measurements are achieved. Using different aptamer switches, this approach can be generalized for measuring other secreted molecules to directly visualize diverse extracellular signaling processes and the biological effects that they trigger in recipient cells.

Resolving the hematopoietic stem cell state by linking functional and molecular assays

One of the most challenging aspects of stem cell research is the reliance on retrospective assays for ascribing function. This is especially problematic for hematopoietic stem cell (HSC) research in which the current functional assay that formally establishes its HSC identity involves long-term serial transplantation assays that necessitate the destruction of the initial cell state many months before knowing that it was, in fact, an HSC. In combination with the explosion of equally destructive single-cell molecular assays, the paradox facing researchers is how to determine the molecular state of a functional HSC when you cannot concomitantly assess its functional and molecular properties. In this review, we will give a historical overview of the functional and molecular assays in the field, identify new tools that combine molecular and functional readouts in populations of HSCs, and imagine the next generation of computational and molecular profiling tools that may help us better link cell function with molecular state.

High-throughput spatiotemporal monitoring of single-cell secretions via plasmonic microwell arrays

Methods for the analysis of cell secretions at the single-cell level only provide semiquantitative endpoint readouts. Here we describe a microwell array for the real-time spatiotemporal monitoring of extracellular secretions from hundreds of single cells in parallel. The microwell array incorporates a gold substrate with arrays of nanometric holes functionalized with receptors for a specific analyte, and is illuminated with light spectrally overlapping with the device's spectrum of extraordinary optical transmission. Spectral shifts in surface plasmon resonance resulting from analyte-receptor bindings around a secreting cell are recorded by a camera as variations in the intensity of the transmitted light while machine-learning-assisted cell tracking eliminates the influence of cell movements. We used the microwell array to characterize the antibody-secretion profiles of hybridoma cells and of a rare subset of antibody-secreting cells sorted from human donor peripheral blood mononuclear cells. High-throughput measurements of spatiotemporal secretory profiles at the single-cell level will aid the study of the physiological mechanisms governing protein secretion.

Spatiotemporal dissection of tumor microenvironment via in situ sensing and monitoring in tumor-on-a-chip

Real-time monitoring in the tumor microenvironment provides critical insights of cancer progression and mechanistic understanding of responses to cancer treatments. However, clinical challenges and significant questions remain regarding assessment of limited clinical tissue samples, establishment of validated, controllable pre-clinical cancer models, monitoring of static versus dynamic markers, and the translation of insights gained from in vitro tumor microenvironments to systematic investigation and understanding in clinical practice. State-of-art tumor-on-a-chip strategies will be reviewed herein, and emerging real-time sensing and monitoring platforms for on-chip analysis of tumor microenvironment will also be examined. The integration of the sensors with tumor-on-a-chip platforms to provide spatiotemporal information of the tumor microenvironment and the associated challenges will be further evaluated. Though optimal integrated systems for in situ monitoring are still in evolution, great promises lie ahead that will open new paradigm for rapid, comprehensive analysis of cancer development and assist clinicians with powerful tools to guide the diagnosis, prognosis and treatment course in cancer.

Mapping secretome-mediated interaction between paired neuron–macrophage single cells

Neuron-immune interaction through secreted factors contributes significantly to the complex microenvironment in the central nervous system that could alter cell functionalities and fates in both physiological and pathological conditions, which remains poorly characterized at the single-cell level. Herein, using a spatially patterned antibody barcode microchip, we realized the mapping of 12 different secretomes, covering cytokines, neurotrophic factors (NFs), and neuron-derived exosomes (NDEs) from high-throughput, paired single cells (≥ 600) simultaneously under normal conditions and an Alzheimer’s disease (AD) model induced with amyloid beta protein 1-42 (Aβ 1–42 ). We applied the platform to analyze the secretion profiles from paired neuron–macrophage and neuron–microglia single cells with human cell lines. We found that pairwise neuron–macrophage interaction would trigger immune responses and attenuate neuron cells’ secretion, while neuron–microglia interaction generally results in opposite outcomes in secretion. When neuron cells are induced with Aβ 1–42 protein into the AD model, both neuron–macrophage and neuron–microglia interactions lead to increased cytokines and NDEs and decreased NFs. Further analysis of AD patients’ serum showed that NDEs were significantly higher in patients’ samples than in the control group, validating our observation from the interaction assay. Furthermore, we resolved previously undifferentiated heterogeneity underlying the secretions from single-neuron cells. We found that the NDE and NF secretion was less dependent on the paracrine signaling between one another and that secretions from neuron cells would attenuate after differentiation with Aβ 1–42 . This study demonstrates the mapping of the different secretomes from paired neuron-immune single cells, providing avenues for understanding how neurons and immune cells interact through the complex secretome network.

High-resolution imaging of protein secretion at the single-cell level using plasmon-enhanced FluoroDOT assay

Secreted proteins mediate essential physiological processes. With conventional assays, it is challenging to map the spatial distribution of proteins secreted by single cells, to study cell-to-cell heterogeneity in secretion, or to detect proteins of low abundance or incipient secretion. Here, we introduce the "FluoroDOT assay," which uses an ultrabright nanoparticle plasmonic-fluor that enables high-resolution imaging of protein secretion. We find that plasmonic-fluors are 16,000-fold brighter, with nearly 30-fold higher signal-to-noise compared with conventional fluorescence labels. We demonstrate high-resolution imaging of different secreted cytokines in the single-plexed and spectrally multiplexed FluoroDOT assay that revealed cellular heterogeneity in secretion of multiple proteins simultaneously. Using diverse biochemical stimuli, including Mycobacterium tuberculosis infection, and a variety of immune cells such as macrophages, dendritic cells (DCs), and DC-T cell co-culture, we demonstrate that the assay is versatile, facile, and widely adaptable for enhancing biological understanding of spatial and temporal dynamics of single-cell secretome.

Optical Sensing Strategies for Probing Single-Cell Secretion

Measuring cell secretion events is crucial to understand the fundamental cell biology that underlies cell-cell communication, migration, proliferation, and differentiation. Although strategies targeting cell populations have provided significant information about live cell secretion, they yield ensemble profiles that obscure intrinsic cell-to-cell variations. Innovation in single-cell analysis has made breakthroughs allowing accurate sensing of a wide variety of secretions and their release dynamics with high spatiotemporal resolution. This perspective focuses on the power of single-cell protocols to revolutionize cell-secretion analysis by allowing real-time and real-space measurements on single live cell resolution. We begin by discussing recent progress on single-cell bioanalytical techniques, specifically optical sensing strategies such as fluorescence-, surface plasmon resonance-, and surface-enhanced Raman scattering-based strategies, capable of in situ real-time monitoring of single-cell released ions, metabolites, proteins, and vesicles. Single-cell sensing platforms which allow for high-throughput high-resolution analysis with enough accuracy are highlighted. Furthermore, we discuss remaining challenges that should be addressed to get a more comprehensive understanding of secretion biology. Finally, future opportunities and potential breakthroughs in secretome analysis that will arise as a result of further development of single-cell sensing approaches are discussed.

Cell-Based Ambient Venturi Autosampling and Matrix-Assisted Laser Desorption Ionization Mass Spectrometric Imaging of Secretory Products

A cell-based ambient Venturi autosampling device was established for the monitoring of dynamic cell secretions in response to chemical stimulations in real time with temporal resolution on the order of a second. Detection of secretory products of cells and screening of bioactive compounds are primarily performed on an ambient autosampling probe and matrix-assisted laser desorption ionization (MALDI) mass spectrometry. It takes advantage of the Venturi effect in which the fluid flowing through an inlet capillary tube is automatically fed into a parallel array of multiple outlet capillaries. Cells are incubated inside the inlet capillary tube that is connected with either a syringe pump or liquid chromatography (LC) for the transfer of single compounds or mixtures, respectively. Secretory products were continuously pushed into the outlet capillaries and then spotted into a compressed thin film of the matrix material 9-aminoacridine for MALDI mass spectrometric imaging. In physiological pH, without the use of high voltages and without the use of chemical derivatizations, this platform can be applied to the direct assay of neurotransmitters or other secretory products released from cells in response to the stimulation of individual compounds or LC-separated eluates of natural mixtures. It provides a new way to identify bioactive compounds with a detection limit down to 0.04 fmol/pixel.

Microscopies Enabled by Photonic Metamaterials

In recent years, the biosensor research community has made rapid progress in the development of nanostructured materials capable of amplifying the interaction between light and biological matter. A common objective is to concentrate the electromagnetic energy associated with light into nanometer-scale volumes that, in many cases, can extend below the conventional Abbé diffraction limit. Dating back to the first application of surface plasmon resonance (SPR) for label-free detection of biomolecular interactions, resonant optical structures, including waveguides, ring resonators, and photonic crystals, have proven to be effective conduits for a wide range of optical enhancement effects that include enhanced excitation of photon emitters (such as quantum dots, organic dyes, and fluorescent proteins), enhanced extraction from photon emitters, enhanced optical absorption, and enhanced optical scattering (such as from Raman-scatterers and nanoparticles). The application of photonic metamaterials as a means for enhancing contrast in microscopy is a recent technological development. Through their ability to generate surface-localized and resonantly enhanced electromagnetic fields, photonic metamaterials are an effective surface for magnifying absorption, photon emission, and scattering associated with biological materials while an imaging system records spatial and temporal patterns. By replacing the conventional glass microscope slide with a photonic metamaterial, new forms of contrast and enhanced signal-to-noise are obtained for applications that include cancer diagnostics, infectious disease diagnostics, cell membrane imaging, biomolecular interaction analysis, and drug discovery. This paper will review the current state of the art in which photonic metamaterial surfaces are utilized in the context of microscopy.

Dielectric nanohole array metasurface for high-resolution near-field sensing and imaging

Dielectric metasurfaces support resonances that are widely explored both for far-field wavefront shaping and for near-field sensing and imaging. Their design explores the interplay between localised and extended resonances, with a typical trade-off between Q-factor and light localisation; high Q-factors are desirable for refractive index sensing while localisation is desirable for imaging resolution. Here, we show that a dielectric metasurface consisting of a nanohole array in amorphous silicon provides a favourable trade-off between these requirements. We have designed and realised the metasurface to support two optical modes both with sharp Fano resonances that exhibit relatively high Q-factors and strong spatial confinement, thereby concurrently optimizing the device for both imaging and biochemical sensing. For the sensing application, we demonstrate a limit of detection (LOD) as low as 1 pg/ml for Immunoglobulin G (IgG); for resonant imaging, we demonstrate a spatial resolution below 1 µm and clearly resolve individual E. coli bacteria. The combined low LOD and high spatial resolution opens new opportunities for extending cellular studies into the realm of microbiology, e.g. for studying antimicrobial susceptibility.

Dielectric metasurfaces have different Q-factor and light localisation requirements for sensing and imaging. Here, the authors present a dielectric metasurface, supporting two optical modes with sharp Fano resonances for high Q-factors and strong spatial confinement, allowing both sensing and imaging.

Using intracellular plasmonics to characterize nanomorphology in human cells

Determining the characteristics and localization of nanoparticles inside cells is crucial for nanomedicine design for cancer therapy. Hyperspectral imaging is a fast, straightforward, reliable, and accurate method to study the interactions of nanoparticles and intracellular components. With a hyperspectral image, we could collect spectral information consisting of thousands of pixels in a short time. Using hyperspectral images, in this work, we developed a label-free technique to detect nanoparticles in different regions of the cell. This technique is based on plasmonic shifts taking place during the interaction of nanoparticles with the surrounding medium. The unique optical properties of gold nanoparticles, localized surface plasmon resonance bands, are influenced by their microenvironment. The LSPR properties of nanoparticles, hence, could provide information on regions in which nanoparticles are distributed. To examine the potential of this technique for intracellular detection, we used three different types of gold nanoparticles: nanospheres, nanostars and Swarna Bhasma (SB), an Indian Ayurvedic/Sidha medicine, in A549 (human non-small cell lung cancer) and HepG2 (human hepatocellular carcinoma) cells. All three types of particles exhibited broader and longer bands once they were inside cells; however, their plasmonic shifts could change depending on the size and morphology of particles. This technique, along with dark-field images, revealed the uniform distribution of nanospheres in cells and could provide more accurate information on their intracellular microenvironment compared to the other particles. The region-dependent optical responses of nanoparticles in cells highlight the potential application of this technique for subcellular diagnosis when particles with proper size and morphology are chosen to reflect the microenvironment effects properly.

Microfluidic Immunoassays for Time-Resolved Measurement of Protein Secretion from Single Cells

Measurement of humoral factors secreted from cells has served as an indispensable method to monitor the states of a cell ensemble because humoral factors play crucial roles in cell-cell interaction and aptly reflect the states of individual cells. Although a cell ensemble consisting of a large number of cells has conventionally been the object of such measurements, recent advances in microfluidic technology together with highly sensitive immunoassays have enabled us to quantify secreted humoral factors even from individual cells in either a population or a temporal context. Many groups have reported various miniaturized platforms for immunoassays of proteins secreted from single cells. This review focuses on the current status of time-resolved assay platforms for protein secretion with single-cell resolution. We also discuss future perspectives of time-resolved immunoassays from the viewpoint of systems biology.

Integrated Microfluidic Device for Functional Secretory Immunophenotyping of Immune Cells

Integrated platforms for automatic assessment of cellular functional secretory immunophenotyping could have a widespread use in the diagnosis, real-time monitoring, and therapy evaluation of several pathologies. We present a microfluidic platform with integrated biosensors and culture chambers to measure cytokine secretion from a consistent and uniform number of immune cells. The biosensor relies on a fluorescence sandwich immunoassay enabled by the mechanically induced trapping of molecular interactions method. The platform contains 32 cell culture chambers, each patterned with an array of 492 microwells, to capture and analyze both adherent and nonadherent immune cells. Multiple stimuli can be delivered to a set of culture chambers. Per chamber, we were able to capture consistently 1113 ± 191 of blood-derived monocytes and neutrophils and 348 ± 37 THP-1 monocytes. Good occupancy efficiencies of ∼70% with a uniformity of ∼90% across all of the culture chambers of the device were achieved. Furthermore, we demonstrate that up to 96% of cells remain viable for the first 48 h. The employment of epoxy-modified glass substrates and active mixing enhanced the biosensing performance compared to the use of bare glass and simple diffusion. Finally, we performed functional secretory analysis of interleukin-8 and tumor necrosis factor alpha from human neutrophils and monocytes, stimulated with various doses of lipopolysaccharide and phorbol 12-myristate 13-acetate-ionomycin, respectively. We foresee the employment of our microfluidic platform in the diagnosis of different pathologies where alterations in cytokine secretion patterns can be used as biomarkers.

Optical Interrogation Techniques for Nanophotonic Biochemical Sensors

The manipulation of light via nanoengineered surfaces has excited the optical community in the past few decades. Among the many applications enabled by nanophotonic devices, sensing has stood out due to their capability of identifying miniscule refractive index changes. In particular, when free-space propagating light effectively couples into subwavelength volumes created by nanostructures, the strongly-localized near-fields can enhance light’s interaction with matter at the nanoscale. As a result, nanophotonic sensors can non-destructively detect chemical species in real-time without the need of exogenous labels. The impact of such nanophotonic devices on biochemical sensor development became evident as the ever-growing research efforts in the field started addressing many critical needs in biomedical sciences, such as low-cost analytical platforms, simple quantitative bioassays, time-resolved sensing, rapid and multiplexed detection, single-molecule analytics, among others. In this review, the optical transduction methods used to interrogate optical resonances of nanophotonic sensors will be highlighted. Specifically, the optical methodologies used thus far will be evaluated based on their capability of addressing key requirements of the future sensor technologies, including miniaturization, multiplexing, spatial and temporal resolution, cost and sensitivity.

Microphysiological sensing platform for an in-situ detection of tissue-secreted cytokines

Understanding the protein-secretion dynamics from single, specific tissues is critical toward the advancement of disease detection and treatments. However, such secretion dynamics remain difficult to measure in vivo due to the uncontrolled contributions from other tissue populations. Here, we describe an integrated platform designed for the reliable, near real-time measurements of cytokines secreted from an in vitro single-tissue model. In our setup, we grow 3D biomimetic tissues to discretize cytokine source, and we separate them from a magnetic microbead-based biosensing system using a Transwell insert. This design integrates physiochemically controlled biological activity, high-sensitivity protein detection (LOD < 20 pg mL-1), and rapid protein diffusion to enable non-invasive, near real-time measurements. To showcase the specificity and sensitivity of the system, we use our setup to probe the inflammatory process related to the protein Interleukine 6 (IL-6) and to the Tumor Necrosis Factor (TNF-α). We show that our setup can monitor the time-dependence profile of IL-6 and TNF-α secretion that results from the electrical and chemical stimulation of 3D skeletal muscle tissues. We demonstrate a novel and affordable methodology for discretizing the secretion kinetics of specific tissues for advancing metabolic-disorder studies and drug-screening applications.

Guided Mode Resonances For Sensing And Imaging

We discuss the latest developments in guided mode resonances for sensing and imaging and compare them to alternative approaches such as plasmonic nanohole arrays.

Highly sensitive and selective light-up fluorescent probe for monitoring gallium and chromium ions in vitro and in vivo

Here reported an NBDT sensor could be effectively responsive to gallium and chromium for bio-imaging in vivo.