Dielectrophoresis-Assisted Self-Digitization Chip for High-Efficiency Single-Cell Analysis.

Single-cell analysis of cell phenotypic information such as surface protein expression and nucleic acid content is essential for understanding heterogeneity within cell populations. Here the design and use of a dielectrophoresis-assisted self-digitization (SD) microfluidics chip is described; it captures single cells in isolated microchambers with high efficiency for single-cell analysis. The self-digitization chip spontaneously partitions aqueous solution into microchambers through a combination of fluidic forces, interfacial tension, and channel geometry. Single cells are guided to and trapped at the entrances of microchambers by dielectrophoresis (DEP) due to local electric field maxima created by an externally applied AC voltage. Excess cells are flushed away, and trapped cells are released into the chambers and prepared for in situ analysis by turning off the external voltage, by running reaction buffer through the chip, and by sealing the chambers with a flow of an immiscible oil phase through the surrounding channels. The use of this device in single-cell analysis is demonstrated by performing single-cell nucleic acid quantitation based on loop-mediated isothermal amplification (LAMP). This platform provides a powerful new tool for single-cell research pertaining to drug discovery. For example, the single-cell genotyping of cancer-related mutant gene observed from the digital chip could be useful biomarker for targeted therapy.

Improving Multicolor Colocalization in Single-Vesicle Flow Cytometry with Vesicle Transit Time.

Immunophenotyping of vesicles, such as extracellular vesicles (EVs), is essential to understanding their origin and biological role. We previously described a custom-built flow analyzer that utilizes a gravity-driven flow, high numerical aperture objective, and micrometer-sized flow channels to reach the sensitivity needed for fast multidimensional analysis of the surface proteins of EVs, even down to the smallest EVs (e.g., ∼30-40 nm). It is difficult to flow focus small EVs, and thus, the transiting EVs exhibit a distribution in particle velocities due to the laminar flow. This distribution of vesicle velocities leads to potentially incorrect results when immunophenotyping nanometer-sized vesicles using cross-correlation analysis (Xcorr), as the order of appearance of the vesicles might not be the same at different spatially offset laser excitation regions. Here, we describe an alternative cross-correlation analysis strategy (Scorr), which uses information on particle transit time across the laser excitation beam width to improve multicolor colocalization in single-vesicle immunoprofiling. We tested the performance of the algorithm for colocalization analysis of multicolor nanobeads and EVs experimentally and via simulations and found that Scorr improved both the efficiency and accuracy of colocalization versus Xcorr. As shown from Monte Carlo simulations, Scorr provided an ∼1.2-4.7-fold increase in the number of colocalized peaks and ensured negligible colocalization of peaks. In silico results were in good agreement with experimental data, which showed an increase in colocalized peaks of ∼1.3-2.5-fold and ∼1.2-2-fold for multicolor beads and EVs, respectively.

BODIPY-based near-infrared semiconducting polymer dot for selective yellow laser-excited cell imaging.

Semiconducting polymer dots (Pdots) with both narrow-band absorption and emission are desirable for multiplexed bioassay applications, but such Pdots with absorption peaks beyond 400 nm are difficult to achieve. Here we describe a donor-energy transfer unit-acceptor (D-ETU-A) design strategy to produce a BODIPY-based Pdot that exhibits simultaneously narrow absorption and emission bands. A green BODIPY (GBDP) unit was employed as the main building block of the polymer backbone, conferring a strong, narrow-band absorption around 551 nm. An NIR720 acceptor provides narrow-band NIR emission. The small Stokes shift of the GBDP donor allows introduction of a benzofurazan-based ETU, resulting in a ternary Pdot with a fluorescence quantum yield of 23.2%, the most efficient yellow-laser excitable Pdot. Due to the strong absorbance band centered at 551 nm and weak absorbance at 405 nm and 488 nm, the Pdot showed high single-particle brightness when excited by a 561 nm (yellow) laser, and selective yellow laser excitation when used to label MCF cells, with much greater brightness when excited at 561 nm than at 405 nm or 488 nm.

Error-Correction Method for High-Throughput Sizing of Nanoscale Vesicles with Single-Molecule Localization Microscopy.

Single-molecule localization microscopy (SMLM) allows super-resolution imaging, mapping, counting, and sizing of biological nanostructures such as cell organelles and extracellular vesicles (EVs), but sizing structures smaller than ∼100 nm can be inaccurate due to single-molecule localization error caused by distortion of the point spread function and limited photon number. Here we demonstrate a method to correct localization error when sizing vesicles and other spherical nanoparticles with SMLM and compare sizing results using two vesicle labeling schemes. We use mean approximation theory to derive a simple equation using full width at half-maximum (FWHM) for correcting particle sizes measured by two-dimensional SMLM, validate the method by sizing streptavidin-coated polystyrene nanobeads with the SMLM technique dSTORM with and without error correction, using transmission electron microscopy (TEM) for comparison, and then apply the method to sizing small seminal EVs. Nanobead sizes measured by dSTORM became increasingly less accurate (larger than TEM values) for beads smaller than 50 nm. The error-correction method reduced the size difference versus TEM from 15% without error correction to 7% with error correction for 40 nm beads, from 44% to 9% for 30 nm beads, and from 66% to 15% for 20 nm beads. Seminal EVs were labeled with a lipophilic membrane dye (MemBright 700) and with an Alexa Fluor 488-anti-CD63 antibody conjugate, and were sized separately using both dyes by dSTORM. Error-corrected exosome diameters were smaller than uncorrected values: 72 nm vs 79 nm mean diameter with membrane dyes; 84 nm vs 97 nm with the antibody-conjugated dyes. The mean error-corrected diameter was 12 nm smaller when using the membrane dye than when using the antibody-conjugated dye likely due to the large size of the antibody. Thus, both the error-correction method and the compact membrane labeling scheme reduce overestimation of vesicle size by SMLM. This error-correction method has a low computational cost as it does not require correction of individual blinking events, and it is compatible with all SMLM techniques (e.g., PALM, STORM, and DNA-PAINT).

High-Precision Mapping of Membrane Proteins on Synaptic Vesicles using Spectrally Encoded Super-Resolution Imaging.

The spatial resolution of single-molecule localization microscopy is limited by the photon number of a single switching event because of the difficulty of correlating switching events dispersed in time. Here we overcome this limitation by developing a new class of photoswitching semiconducting polymer dots (Pdots) with structured and highly dispersed single-particle spectra. We imaged the Pdots at the first and the second vibronic emission peaks and used the ratio of peak intensities as a spectral coding. By correlating switching events using the spectral coding and performing 4-9 frame binning, we achieved a 2-3 fold experimental resolution improvement versus conventional superresolution imaging. We applied this method to count and map SV2 and proton ATPase proteins on synaptic vesicles (SVs). The results reveal that these proteins are trafficked and organized with high precision, showing unprecedented level of detail about the composition and structure of SVs.

A reinforced PDMS mold for hot embossing of cyclic olefin polymer in the fabrication of microfluidic chips.

Hot embossing is a cost-effective and flexible fabrication technology with high replication accuracy for feature sizes as small as 50 nm. Here we develop a reinforced polydimethylsiloxane (PDMS) mold for hot embossing of cyclic olefin polymer (COP) sheets in the fabrication of microfluidic chips and demonstrate the method by fabricating chips for automated sample digitization in digital nucleic acid assays. The PDMS is hardened by adding an investment powder as a dopant and is constrained with an aluminum frame to prevent lateral expansion during hot pressing. The reinforced PDMS mold demonstrated excellent performance in hot embossing (180 °C, 103 kPa, 5 min) for micropatterning COP sheets, with highly reproducible features as small as 10 µm (width of draining channel). In contrast, the microscale features were inconsistent and distorted when omitting either the investment powder or frame from the PDMS mold. COP chips were assembled by thermally bonding patterned and unpatterned COP sheets. We tested the performance of the COP chip for automated sample digitization in a digital LAMP assay used to quantify human papillomavirus-18 (HPV-18) DNA. A mixture of nucleic acid amplification reagents was loaded into the main channel of the chip using a syringe pump, then the solution was spontaneously partitioned into chambers (∼0.6 nL), which were then isolated by flowing oil through the chip. The digital LAMP assay produced accurately absolute quantitation of DNA at concentrations ranging from 10 to 1000 copies per µL. The strategy presented here provides a simple, low-cost method to prepare molds for hot embossing, which facilitates rapid validation of microfluidic designs.

Near-Infrared Optical Transducer for Dynamic Imaging of Cerebrospinal Fluid Glucose in Brain Tumor.

Aberrant cerebral glucose metabolism is related to many brain diseases, especially brain tumor. However, it remains challenging to measure the dynamic changes in cerebral glucose. Here, we developed a near-infrared (NIR) optical transducer to sensitively monitor the glucose variations in cerebrospinal fluid in vivo. The transducer consists of an oxygen-sensitive nanoparticle combined with glucose oxidase (GOx), yielding highly sensitive NIR phosphorescence in response to blood glucose change. We demonstrated long-term continuous glucose monitoring by using the NIR transducer. After subcutaneous implantation, the glucose transducer provides a strong luminescence signal that can continuously monitor blood glucose fluctuations for weeks. By using the NIR emission of the transducer, we further observed abnormal dynamic changes in cerebrospinal fluid glucose and quantitatively assessed cerebral glucose uptake rates in transgenic mice bearing brain tumors. This study provides a promising method for the diagnosis of various metabolic diseases with altered glucose metabolism.

Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research.

The extracellular RNA communication consortium (ERCC) is an NIH-funded program aiming to promote the development of new technologies, resources, and knowledge about exRNAs and their carriers. After Phase 1 (2013-2018), Phase 2 of the program (ERCC2, 2019-2023) aims to fill critical gaps in knowledge and technology to enable rigorous and reproducible methods for separation and characterization of both bulk populations of exRNA carriers and single EVs. ERCC2 investigators are also developing new bioinformatic pipelines to promote data integration through the exRNA atlas database. ERCC2 has established several Working Groups (Resource Sharing, Reagent Development, Data Analysis and Coordination, Technology Development, nomenclature, and Scientific Outreach) to promote collaboration between ERCC2 members and the broader scientific community. We expect that ERCC2's current and future achievements will significantly improve our understanding of exRNA biology and the development of accurate and efficient exRNA-based diagnostic, prognostic, and theranostic biomarker assays.

Ultrabright Pdots with a Large Absorbance Cross Section and High Quantum Yield.

Semiconducting polymer dots (Pdots) are increasingly used in biomedical applications due to their extreme single-particle brightness, which results from their large absorption cross section (σ). However, the quantum yield (Φ) of Pdots is typically below 40% due to aggregation-induced self-quenching. One approach to reducing self-quenching is to use FRET between the donor (D) and acceptor (A) groups within a Pdot; however, Φ values of FRET-based Pdots remain low. Here, we demonstrate an approach to achieve ultrabright FRET-based Pdots with simultaneously high σ and Φ. The importance of self-quenching was revealed in a non-FRET Pdot: adding 30 mol % of a nonabsorbing polyphenyl to a poly(9,9-dioctylfluorene) (PFO) Pdot increased Φ from 13.4 to 71.2%, yielding an ultrabright blue-emitting Pdot. We optimized the brightness of FRET-based Pdots by exploring different D/A combinations and ratios with PFO and poly[(9,9-dioctylfluorenyl-2,7-diyl)-co-(1,4-phenylene)] (PFP) as donor polymers and poly[(9,9-dioctyl-2,7-divinylenefluorenylene)-alt-co-(1,4-phenylene)] (PFPV) and poly[(9,9-dioctylfluorenyl-2,7-diyl)-alt-co-(1,4-benzo-{2,1',3}-thiadiazole)] (PFBT) as acceptor polymers, with a fixed concentration of poly(styrene-co-maleic anhydride) as surfactant polymer. Ultrabright blue-emitting Pdots possessing high Φ (73.1%) and σ (σR = σabs/σall, 97.5%) were achieved using PFP/PFPV Pdots at a low acceptor content (A/[D + A], 2.5 mol %). PFP/PFPV Pdots were 1.8 times as bright as PFO/PFPV Pdots due to greater coverage of acceptor absorbance by donor emission─a factor often overlooked in D/A pair selection. Ultrabright green-emitting PFO Pdots (Φ = 76.0%, σR = 92.5%) were obtained by selecting an acceptor (PFBT) with greater spectral overlap with PFO. Ultrabright red-emitting Pdots (Φ = 64.2%, σR = 91.0%) were achieved by blending PFO, PFBT, and PFTBT to create a cascade FRET Pdot at a D:A1:A2 molar ratio of 61:5:1. These blue, green, and red Pdots are among the brightest Pdots reported. This approach of using a small, optimized amount of FRET acceptor polymer with a large donor-acceptor spectral overlap can be generalized to produce ultrabright Pdots with emissions that span the visible spectrum.

Long-Term In Vivo Glucose Monitoring by Polymer-Dot Transducer in an Injectable Hydrogel Implant.

Optical sensors have attracted a great deal of interest for glucose detection. However, their practical applications for continuous glucose monitoring are still constrained by operational reliability in subcutaneous tissues. Here, we show an implantable hydrogel platform embedded with luminescent polymer dots (Pdots) for sensitive and long-term glucose monitoring. We use Pdot transducer in a polyacrylamide hydrogel matrix to construct an implantable platform. The hydrogel-Pdot transducer showed bright luminescence with ratiometric response to glucose changes. The in vitro and in vivo sensitivities of the hydrogel implant were enhanced by varying the enzyme concentration and injection volume. After implantation, the hydrogel with Pdot transducer remained at the implanted site without migration for 1 month and can be removed from the subcutaneous tissue for further analysis. Our results indicate that the hydrogel-Pdot platform maintains the intrinsic sensing property with excellent stability during 1 month implantation, while fibrous capsule formation on the implant in some cases needs to be solved for long-term continuous glucose monitoring.

Precision Medicine in Low- and Middle-Income Countries.

Most cancer cases occur in low- and middle-income countries (LMICs). The sophisticated technical and human infrastructure needed for optimal diagnosis, treatment, and monitoring of cancers is difficult enough in affluent countries; it is especially challenging in LMICs. In Western, educated, industrial, rich, democratic countries, there is a growing emphasis on and success with precision medicine, whereby targeted therapy is directed at cancers based on the specific genetic lesions in the cancer. Can such precision approaches be delivered in LMICs? We offer some examples of novel partnerships and creative solutions that suggest that precision medicine may be possible in LMICs given heavy doses of will, creativity, and persistence and a little luck.

Digital Quantification of Human Viral RNA and DNA Using a Self-Digitization Chip.

Digital nucleic acid quantitation methods show excellent sensitivity and specificity for pathogen detection. Droplet digital PCR (ddPCR) is the most advanced digital nucleic acid quantitation method and has been commercialized, but is not suitable for many point-of-care applications due to its complex instrumentation. Here we describe a simple microfluidics-based self-digitization (SD) chip for quantifying nucleic acids at the point of care with minimal instrumentation. We demonstrate the clinical diagnostic capability of this platform by applying it to quantifying human viral DNA and RNA. SD chips with a range of well numbers and volumes are tested, and isothermal methods are used to amplify the DNA and RNA to a detectable level. Sample concentration is determined based on the measured volume in the wells and the number of wells with fluorescence greater than a threshold based on a Poisson distribution. Concentration measurements over the low concentration range of 0-100 molecules/µL showed a strong correlation (R2 = 0.99) with measurements using a real-time PCR assay, demonstrating the sensitivity and specificity of the SD chip platform.

Rigor and reproducibility: status and challenges for single vesicle analysis.

This report summarises the presentations and activities of the SELECTBIO Workshop on Rigor and Reproducibility in EV Research and Single EV Analysis held in San Diego, USA, in December 2021. The motivation for the session was the recognition that progress in the extracellular vesicle (EV) field is limited by the availability of rigorous and reproducible EV measurement tools. These tools are absolutely required for EVs to evolve from a research lab curiosity to something that will improve our ability to understand, diagnose, treat, and prevent disease. The program focused on guidelines for EV measurement and characterization as laid out in the recent MISEV2018 and MIFlowCyt-EV publications, their implementation in routine practice, and their continued evolution as new EV measurement technologies are introduced. The conclusion of the workshop was that more effort focused on pre-analytical issues and benchmarking of isolation methods is needed to strengthen collaborations and advance more effective biomarkers.

Capillary-Mediated Single-Cell Dispenser.

Single-cell manipulation, sorting, and dispensing into multiwell plates is useful for single-cell multiomics studies. Here, we develop a single-cell dispenser inspired by electrohydrodynamic jet printing that achieves accurate droplet generation and single-cell sorting and dispensing using fused silica capillary tubing as both the optical detection window and nozzle for droplet dispensing. Parameters that affect droplet dispensing performance-capillary inner and outer diameter, flow rate, applied voltage, and solution properties-were optimized systematically with COMSOL simulations and experimentation. Small (5-10 nL) droplets were obtained by using 100-µm inner diameter and 160-µm outer diameter capillary tubing and allowed efficient encapsulation and dispensing of single cells. We demonstrate an application of this easy-to-assemble single-cell dispenser by sorting and dispensing cells into multiwell plates for single-cell PCR analysis.

Monitoring Metabolites Using an NAD(P)H-sensitive Polymer Dot and a Metabolite-Specific Enzyme.

We introduce an NAD(P)H-sensitive polymer dot (Pdot) biosensor for point-of-care monitoring of metabolites. The Pdot is combined with a metabolite-specific NAD(P)H-dependent enzyme that catalyzes the oxidation of the metabolite, generating NAD(P)H. Upon UV illumination, the NAD(P)H quenches the fluorescence emission of Pdot at 627 nm via electron transfer, and also fluoresces at 458 nm, resulting in a shift from red to blue emission at higher NAD(P)H concentrations. Metabolite concentration is quantified ratiometrically-based on the ratio of blue-to-red channel emission intensities, with a digital camera-with high sensitivity and specificity. We demonstrate phenylalanine biosensing in human plasma for a phenylketonuria screening test, quantifying several other disease-related metabolites (lactate, glucose, glutamate, and ß-hydroxybutyrate), and a paper-based assay with smartphore imaging for point-of-care use.

High-Throughput Counting and Superresolution Mapping of Tetraspanins on Exosomes Using a Single-Molecule Sensitive Flow Technique and Transistor-like Semiconducting Polymer Dots.

A method for high-throughput counting and superresolution mapping of surface proteins on exosomes is described. The method combines a single-molecule sensitive flow technique and an adaptive superresolution imaging method. Exosomes stained with membrane dye and dye-conjugated antibodies were analyzed using a microfluidic platform at a flow rate of 100 exosome s-1 to determine size and protein copy number. Superresolution mapping was performed with exosomes labeled with novel transistor-like, semiconducting polymer dots (Pdots), which exhibit spontaneous blinking with <5 nm localization error and a broad range of optical-adjustable duty cycles. Based on the copy numbers extracted from the flow analysis, the switch-on frequency of the Pdots were finely adjusted so that structures of hundreds of exosomes were obtained within five minutes. The high throughput and high sensitivity of this method offer clear advantages for characterization of exosomes and similar biological vesicles.

ß-arrestin-dependent PI(4,5)P2 synthesis boosts GPCR endocytosis.

ß-arrestins regulate many cellular functions including intracellular signaling and desensitization of G protein-coupled receptors (GPCRs). Previous studies show that ß-arrestin signaling and receptor endocytosis are modulated by the plasma membrane phosphoinositide lipid phosphatidylinositol-(4, 5)-bisphosphate (PI(4,5)P2). We found that ß-arrestin also helped promote synthesis of PI(4,5)P2 and up-regulated GPCR endocytosis. We studied these questions with the Gq-coupled protease-activated receptor 2 (PAR2), which activates phospholipase C, desensitizes quickly, and undergoes extensive endocytosis. Phosphoinositides were monitored and controlled in live cells using lipid-specific fluorescent probes and genetic tools. Applying PAR2 agonist initiated depletion of PI(4,5)P2, which then recovered during rapid receptor desensitization, giving way to endocytosis. This endocytosis could be reduced by various manipulations that depleted phosphoinositides again right after phosphoinositide recovery: PI(4)P, a precusor of PI(4,5)P2, could be depleted at either the Golgi or the plasma membrane (PM) using a recruitable lipid 4-phosphatase enzyme and PI(4,5)P2 could be depleted at the PM using a recruitable 5-phosphatase. Endocytosis required the phosphoinositides. Knock-down of ß-arrestin revealed that endogenous ß-arrestin normally doubles the rate of PIP5-kinase (PIP5K) after PAR2 desensitization, boosting PI(4,5)P2-dependent formation of clathrin-coated pits (CCPs) at the PM. Desensitized PAR2 receptors were swiftly immobilized when they encountered CCPs, showing a dwell time of ∼90 s, 100 times longer than for unactivated receptors. PAR2/ß-arrestin complexes eventually accumulated around the edges or across the surface of CCPs promoting transient binding of PIP5K-Iγ. Taken together, ß-arrestins can coordinate potentiation of PIP5K activity at CCPs to induce local PI(4,5)P2 generation that promotes recruitment of PI(4,5)P2-dependent endocytic machinery.

Reversible Ratiometric NADH Sensing Using Semiconducting Polymer Dots.

Reduced nicotinamide adenine dinucleotide (NADH) is a key coenzyme in living cells due to its role as an electron carrier in redox reactions, and its concentration is an important indicator of cell metabolic state. Abnormal NADH levels are associated with age-related metabolic diseases and neurodegenerative disorders, creating a demand for a simple, rapid analytical method for point-of-care NADH sensing. Here we develop a series of NADH-sensitive semiconducting polymer dots (Pdots) as nanoprobes for NADH measurement, and test their performance in vitro and in vivo. NADH sensing is based on electron transfer from semiconducting polymer chains in the Pdot to NADH upon UV excitation, quenching Pdot fluorescence emission. In polyfluorene-based Pdots, this mechanism resulted in an on-off NADH sensor; in DPA-CNPPV Pdots, UV excitation resulted in NADH-sensitive emission at two wavelengths, enabling ratiometric detection. Ratiometric NADH detection using DPA-CNPPV Pdots exhibits high sensitivity (3.1 µM limit of detection), excellent selectivity versus other analytes, reversibility, and a fast response (less than 5 s). We demonstrate applications of the ratiometric NADH-sensing Pdots including smartphone-based NADH imaging for point-of-care use.

Sizing Extracellular Vesicles Using Membrane Dyes and a Single Molecule-Sensitive Flow Analyzer.

Extracellular vesicles (EVs) are membranous particles released by most cells in our body, which are involved in many cell-to-cell signaling processes. Given the nanometer sizes and heterogeneity of EVs, highly sensitive methods with single-molecule resolution are fundamental to investigating their biophysical properties. Here, we demonstrate the sizing of EVs using a fluorescence-based flow analyzer with single-molecule sensitivity. Using a dye that selectively partitions into the vesicle's membrane, we show that the fluorescence intensity of a vesicle is proportional to its diameter. We discuss the constraints in sample preparation which are inherent to sizing nanoscale vesicles with a fluorescent membrane dye and propose several guidelines to improve data consistency. After optimizing staining conditions, we were able to measure the size of vesicles in the range ∼35-300 nm, covering the spectrum of EV sizes. Lastly, we developed a method to correct the signal intensity from each vesicle based on its traveling speed inside the microfluidic channel, by operating at a high sampling rate (10 kHz) and measuring the time required for the particle to cross the laser beam. Using this correction, we obtained a threefold greater accuracy in EV sizing, with a precision of ±15-25%.

Multimode Time-Resolved Superresolution Microscopy Revealing Chain Packing and Anisotropic Single Carrier Transport in Conjugated Polymer Nanowires.

Here, we developed a novel, multimode superresolution method to perform full-scale structural mapping and measure the energy landscape for single carrier transport along conjugated polymer nanowires. Through quenching of the local emission, the motion of a single photogenerated hole was tracked using blinking-assisted localization microscopy. Then, utilizing binding and unbinding dynamics of quenchers onto the nanowires, local emission spectra were collected sequentially and assembled to create a superresolution map of emission sites throughout the structure. The hole polaron trajectories were overlaid with the superresolution maps to correlate structures with charge transport properties. Using this method, we compared the efficiency of inter- and intrachain hole transport inside the nanowires and for the first time directly measured the depth of carrier traps originated from torsional disorder and chemical defects.