Pushing the limits of detection for proteins secreted from single cells using quantum dots

Recent advances in microfluidics for single-cell functional proteomics

Single-cell proteomics (SCP) reveals phenotypic heterogeneity by profiling individual cells, their biological states and functional outcomes upon signaling activation that can hardly be probed via other omics characterizations. This has become appealing to researchers as it enables an overall more holistic view of biological details underlying cellular processes, disease onset and progression, as well as facilitates unique biomarker identification from individual cells. Microfluidic-based strategies have become methods of choice for single-cell analysis because they allow facile assay integrations, such as cell sorting, manipulation, and content analysis. Notably, they have been serving as an enabling technology to improve the sensitivity, robustness, and reproducibility of recently developed SCP methods. Critical roles of microfluidics technologies are expected to further expand rapidly in advancing the next phase of SCP analysis to reveal more biological and clinical insights. In this review, we will capture the excitement of the recent achievements of microfluidics methods for both targeted and global SCP, including efforts to enhance the proteomic coverage, minimize sample loss, and increase multiplexity and throughput. Furthermore, we will discuss the advantages, challenges, applications, and future prospects of SCP.

Multiplexed Immunoassay Using Quantum Dots to Monitor Proteins Secreted from Single Cells at Near-Single Molecule Resolution

Single-cell secretion studies find important applications in molecular diagnostics, therapeutic target identification, and basic biology research. One increasingly important area of research is non-genetic cellular heterogeneity, a phenomenon that can be studied by assessing secretion of soluble effector proteins from single cells. This is particularly impactful for immune cells, as secreted proteins such as cytokines, chemokines, and growth factors are the gold standard for identifying phenotype. Current methods that rely upon immunofluorescence suffer from low detection sensitivity, requiring thousands of molecules to be secreted per cell. We have developed a quantum dot (QD)-based single-cell secretion analysis platform that can be used in different sandwich immunoassay formats to dramatically lower detection threshold, such that only one to a few molecules need be secreted per cell. We have also expanded this work to include multiplexing capabilities for different cytokines and employed this platform to study macrophage polarization under different stimuli at the single-cell level.

Quantum dots in the biomedical world: A smart advanced nanocarrier for multiple venues application

Quantum dots (QDs) are semiconducting nanoparticles having different optical and electrical properties when compared to larger particles. They exhibit photoluminescence when irradiated with ultraviolet light, which is due to the transition of an excited electron from the valence band to the conductance band followed by the return of the exciting electron back into the valence band. The size and material of QDs can affect their optical and other properties too. The QDs possess special attributes like high brightness, protection from photobleaching, photostability, color tunability, low toxicity, low production cost, a multiplexing limit, and a high surface-to-volume proportion, which make them a promising tool for biomedical applications. Here, in this study, we summarize the utilization of QDs in different applications including bioimaging, diagnostics, immunostaining, single-cell analysis, drug delivery, and protein detection. Moreover, we discuss the advantages and challenges of using QDs in biomedical applications when compared with other conventional tools.

Antibody-functionalized aluminum oxide-coated particles targeting neutrophil receptors in a multifrequency microfluidic impedance cytometer

Personalized diagnostics of infectious diseases require monitoring disease progression due to their ever-changing physiological conditions and the multi-faceted organ system mechanisms involved in disease pathogenesis. In such instances, the recommended clinical strategies involve multiplexing data collection from critical biomarkers related to a patient's conditions along with longitudinal frequent patient monitoring. Numerous detection technologies exist both in research and commercial settings to monitor these conditions, however, they fail to provide biomarker multiplexing ability with design and data processing simplicity. For a recently conceived multiplexing biomarker modality, this work demonstrates the use of electrically sensitive microparticles targeting and identifying membrane receptors on leukocytes using a single detection source, with a high potential for multiplexing greater than any existing impedance-based single-detection scheme. Here, polystyrene microparticles are coated with varying thicknesses of metal oxides, which generate quantifiable impedance shifts when exposed to multifrequency electric fields depending on the metal oxide thickness. Using multifrequency impedance cytometry, these particles can be measured and differentiated rapidly across one coplanar electrode scheme. After surface-functionalizing particles with antibodies targeting CD11b and CD66b receptors, the particles are combined with isolated neutrophils to measure receptor expression. A combination of data analysis techniques including multivariate analysis, supervised machine learning, and unsupervised machine learning was able to accurately differentiate samples with up to 91% accuracy. This proof-of-concept study demonstrates the potential for these oxide-coated particles for enumerating specific leukocytes enabling multiplexing. Further, additional coating thicknesses or different metal oxide materials can enable a compendium of multiplexing targeting resource to be used to develop a high-multiplexing sensor for targeting membrane receptor expression.

Multiplexed Detection of Secreted Cytokines at near-Molecular Resolution Elucidates Macrophage Polarization Heterogeneity

Monitoring the secretion of proteins from single cells can provide important insights into how cells respond to their microenvironment. This is particularly true for immune cells, which can exhibit a large degree of response heterogeneity. Microfabricated well arrays provide a powerful and versatile method to assess the secretion of cytokines, chemokines, and growth factors from single cells, but detection sensitivity has been limited to high levels on the order of 10,000 per cell. Recently, we reported a quantum dot-based immunoassay that lowered the detection limit for the cytokine TNF-α to concentrations to nearly the single-cell level. Here, we adapted this detection method to three additional targets while maintaining high detection sensitivity. Specifically, we detected MCP-1, TGF-β, IL-10, and TNF-α using quantum dots with different emission spectra, each of which displayed a detection threshold in the range of 1-10 fM or ∼1-2 molecules per well. We then quantified secretion of all four proteins from single macrophage cells that were stimulated toward a pro-inflammatory state with lipopolysaccharide (LPS) or toward a pro-healing state with both LPS and interleukin 4 (IL-4). We found that MCP-1 and TGF-β were predominantly secreted at high levels only (>10,000 molecules/cell), while a substantial number of cells secreted IL-10 and TNF-α at lower levels that could only be detected using our method. Subsequent principal component and cluster analysis revealed that secretion profiles could be classified as either exclusively pro-inflammatory, including MCP-1 and/or TNF-α, or more subtle responses displaying both pro-healing and pro-inflammatory characters. Our results highlight the heterogeneous and nondiscrete nature of macrophage phenotypes following in vitro stimulation of a cell line. Future work will focus on expanding the multiplexing capacity by extending emission spectra bandwidth and/or spatially barcoding capture antibodies, as well as evaluating the enhanced detection sensitivity capabilities with normal and diseased immune cell populations in vitro and in vivo.

Attomolar analyte sensing techniques (AttoSens): a review on a decade of progress on chemical and biosensing nanoplatforms

Detecting the ultra-low abundance of analytes in real-life samples, such as biological fluids, water, soil, and food, requires the design and development of high-performance biosensing modalities. The breakthrough efforts from the scientific community have led to the realization of sensing technologies that measure the analyte's ultra-trace level, with relevant sensitivity, selectivity, response time, and sampling efficiency, referred to as Attomolar Analyte Sensing Techniques (AttoSens) in this review. In an AttoSens platform, 1 aM detection corresponds to the quantification of 60 target analyte molecules in 100 μL of sample volume. Herein, we review the approaches listed for various sensor probe design, and their sensing strategies that paved the way for the detection of attomolar (aM: 10^-18 M) concentration of analytes. A summary of the technological advances made by the diverse AttoSens trends from the past decade is presented.

Point-of-critical-care diagnostics for sepsis enabled by multiplexed micro and nanosensing technologies

Sepsis is responsible for the highest economic and mortality burden in critical care settings around the world, prompting the World Health Organization in 2018 to designate it as a global health priority. Despite its high universal prevalence and mortality rate, a disproportionately low amount of sponsored research funding is directed toward diagnosis and treatment of sepsis, when early treatment has been shown to significantly improve survival. Additionally, current technologies and methods are inadequate to provide an accurate and timely diagnosis of septic patients in multiple clinical environments. For improved patient outcomes, a comprehensive immunological evaluation is critical which is comprised of both traditional testing and quantifying recently proposed biomarkers for sepsis. There is an urgent need to develop novel point-of-care, low-cost systems which can accurately stratify patients. These point-of-critical-care sensors should adopt a multiplexed approach utilizing multimodal sensing for heterogenous biomarker detection. For effective multiplexing, the sensors must satisfy criteria including rapid sample to result delivery, low sample volumes for clinical sample sparring, and reduced costs per test. A compendium of currently developed multiplexed micro and nano (M/N)-based diagnostic technologies for potential applications toward sepsis are presented. We have also explored the various biomarkers targeted for sepsis including immune cell morphology changes, circulating proteins, small molecules, and presence of infectious pathogens. An overview of different M/N detection mechanisms are also provided, along with recent advances in related nanotechnologies which have shown improved patient outcomes and perspectives on what future successful technologies may encompass. This article is categorized under: Diagnostic Tools > Biosensing.

Pushing the detection limits: strategies towards highly sensitive optical-based protein detection

Proteins are one of the main constituents of living cells. Studying the quantities of proteins under physiological and pathological conditions can give valuable insights into health status, since proteins are the functional molecules of life. To be able to detect and quantify low-abundance proteins in biofluids for applications such as early disease diagnostics, sensitive analytical techniques are desired. An example of this application is using proteins as biomarkers for detecting cancer or neurological diseases, which can provide early, lifesaving diagnoses. However, conventional methods for protein detection such as ELISA, mass spectrometry, and western blotting cannot offer enough sensitivity for certain applications. Recent advances in optical-based micro- and nano-biosensors have demonstrated promising results to detect proteins at low quantities down to the single-molecule level, shining lights on their capacities for ultrasensitive disease diagnosis and rare protein detection. However, to date, there is a lack of review articles synthesizing and comparing various optical micro- and nano-sensing methods of enhancing the limits of detections of the antibody-based protein assays. The purpose of this article is to critically review different strategies of improving assay sensitivity using miniaturized biosensors, such as assay miniaturization, improving antibody binding capacity, sample purification, and signal amplification. The pros and cons of different methods are compared, and the future perspectives of this research field are discussed.

Edge-Enhanced Microwell Immunoassay for Highly Sensitive Protein Detection

Highly sensitive biosensors that can detect low concentrations of protein biomarkers at the early stages of diseases or proteins secreted from single cells are of importance for disease diagnosis and treatment assessment. This work reports a new signal amplification mechanism, that is, edge enhancement based on the vertical sidewalls of microwells for ultra-sensitive protein detection. The fluorescence emission at the edge of the microwells is highly amplified due to the microscopic axial resolution (depth of field) and demonstrates a microring effect. The enhanced fluorescence intensity from microrings is calibrated for bovine serum albumin detection, which shows a 6-fold sensitivity enhancement and a lower limit of detection at the microwell edge, compared to those obtained on a flat surface. The microwell chip is used to separate single cells, and the wall of each microwell is used to detect interferon-γ secretion from T cells stimulated with a peptide and whole cancer cells. Given its edge-enhancement ability, the microwell technique can be a highly sensitive biosensing platform for disease diagnosis at an early stage and for assessing potential treatments at the single-cell level.

Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics

Biological systems are composed of heterogeneous populations of cells that intercommunicate to form a functional living tissue. Biological function varies greatly across populations of cells, as each single cell has a unique transcriptome, proteome, and metabolome that translates to functional differences within single species and across kingdoms. Over the past decade, substantial advancements in our ability to characterize omic profiles on a single cell level have occurred, including in multiple spectroscopic and mass spectrometry (MS)-based techniques. Of these technologies, spatially resolved mass spectrometry approaches, including mass spectrometry imaging (MSI), have shown the most progress for single cell proteomics and metabolomics. For example, reporter-based methods using heavy metal tags have allowed for targeted MS investigation of the proteome at the subcellular level, and development of technologies such as laser ablation electrospray ionization mass spectrometry (LAESI-MS) now mean that dynamic metabolomics can be performed in situ. In this Perspective, we showcase advancements in single cell spatial metabolomics and proteomics over the past decade and highlight important aspects related to high-throughput screening, data analysis, and more which are vital to the success of achieving proteomic and metabolomic profiling at the single cell scale. Finally, using this broad literature summary, we provide a perspective on how the next decade may unfold in the area of single cell MS-based proteomics and metabolomics.

Measuring single-cell protein secretion in immunology: Technologies, advances, and applications

The dynamics, nature, strength, and ultimately protective capabilities of an active immune response are determined by the extracellular constitution and concentration of various soluble factors. Generated effector cells secrete such mediators, including antibodies, chemo‐ and cytokines to achieve functionality. These secreted factors organize the individual immune cells into functional tissues, initiate, orchestrate, and regulate the immune response. Therefore, a single‐cell resolved analysis of protein secretion is a valuable tool for studying the heterogeneity and functionality of immune cells. This review aims to provide a comparative overview of various methods to characterize immune reactions by measuring single‐cell protein secretion. Spot‐based and cytometry‐based assays, such as ELISpot and flow cytometry, respectively, are well‐established methods applied in basic research and clinical settings. Emerging novel technologies, such as microfluidic platforms, offer new ways to measure and exploit protein secretion in immune reactions. Further technological advances will allow the deciphering of protein secretion in immunological responses with unprecedented detail, linking secretion to functionality. Here, we summarize the development and recent advances of tools that allow the analysis of protein secretion at the single‐cell level, and discuss and contrast their applications within immunology.

Design of a Multiplexed Analyte Biosensor using Digital Barcoded Particles and Impedance Spectroscopy

Multiplexing allows quantifying multiple analytes in a single step, providing advantages over individual testing through shorter processing time, lower sample volume, and reduced cost per test. Currently, flow cytometry is the gold standard for biomedical multiplexing, but requires technical training, extensive data processing, and expensive operational and capital costs. To solve this challenge, we designed digital barcoded particles and a microfluidic architecture for multiplexed analyte quantification. In this work, we simulate and model non-fluorescence-based microfluidic impedance detection with a single excitation and detection scheme using barcoded polymer microparticles. Our barcoded particles can be designed with specific coding regions and generate numerous distinct patterns enabling digital barcoding. We found that signals based on adhered microsphere position and relative orientation were evaluated and separated based on their associated electrical signatures and had a 7 µm microsphere limit of detection. Our proposed microfluidic system can enumerate micron-sized spheres in a single assay using barcoded particles of various configurations. As representation of blood cells, the microsphere concentrations may provide useful information on disease onset and progression. Such sensors may be used for diagnostic and management of common critical care diseases like sepsis, acute kidney injury, urinary tract infections, and HIV/AIDS.

A Nanoparticle-Based Affinity Sensor that Identifies and Selects Highly Cytokine-Secreting Cells

We developed a universal method termed OnCELISA to detect cytokine secretion from individual cells by applying a capture technology on the cell membrane. OnCELISA uses fluorescent magnetic nanoparticles as assay reporters that enable detection on a single-cell level in microscopy and flow cytometry and fluorimetry in cell ensembles. This system is flexible and can be modified to detect different cytokines from a broad range of cytokine-secreting cells. Using OnCELISA we have been able to select and sort highly cytokine-secreting cells and identify cytokine-secreting expression profiles of different cell populations in vitro and ex vivo. We show that this system can be used for ultrasensitive monitoring of cytokines in the complex biological environment of atherosclerosis that contains multiple cell types. The ability to identify and select cell populations based on their cytokine expression characteristics is valuable in a host of applications that require the monitoring of disease progression.

Aptamer Induced Multicolored AuNCs-WS2 "Turn on" FRET Nano Platform for Dual-Color Simultaneous Detection of AflatoxinB1 and Zearalenone

Mycotoxins posit serious threats to human and animal health, and numerous efforts have been performed to detect the multiple toxins by a single diagnostic approach. To best of our knowledge, for the first time, we synthesized an aptamer induced "turn on" fluorescence resonance energy transfer (FRET) biosensor using dual-color gold nanoclusters (AuNCs), l-proline, and BSA synthesized AuNCs (Lp-AuNCs and BSA-AuNCs), with WS₂ nanosheet for simultaneous recognition of aflatoxinB₁ (AFB₁) and zearalenone (ZEN) by single excitation. Here, AFB₁ aptamer stabilized blue-emitting AuNCs (AFB₁-apt-Lp-AuNCs) (at 442 nm) and ZEN aptamer functionalized with red-colored AuNCs (ZEN-apt-BSA-AuNCs) (at 650 nm) were employed as an energy donor and WS₂ nanosheet as a fluorescence quencher. With the addition of AFB₁ and ZEN, the change in fluorescence intensity (F.I) was recorded at 442 and 650 nm and can be used for simultaneous recognition with a detection limit of 0.34 pg mL^-1 (R² = 0.9931) and 0.53 pg mL^-1 (R² = 0.9934), respectively. Most importantly, the semiquantitative determination of AFB₁ and ZEN can also be realized through photovisualization. The current approach paves a new way to develop sensitive, selective, and convenient metal nanocluster-based fluorescent "switch-on" probes with potential applications in multipurpose biosensing.

Recent advances in microfluidic platforms for single-cell analysis in cancer biology, diagnosis and therapy

Understanding molecular, cellular, genetic and functional heterogeneity of tumors at the single-cell level has become a major challenge for cancer research. The microfluidic technique has emerged as an important tool that offers advantages in analyzing single-cells with the capability to integrate time-consuming and labour-intensive experimental procedures such as single-cell capture into a single microdevice at ease and in a high-throughput fashion. Single-cell manipulation and analysis can be implemented within a multi-functional microfluidic device for various applications in cancer research. Here, we present recent advances of microfluidic devices for single-cell analysis pertaining to cancer biology, diagnostics, and therapeutics. We first concisely introduce various microfluidic platforms used for single-cell analysis, followed with different microfluidic techniques for single-cell manipulation. Then, we highlight their various applications in cancer research, with an emphasis on cancer biology, diagnosis, and therapy. Current limitations and prospective trends of microfluidic single-cell analysis are discussed at the end.