Sample Throughput Research Articles

Multiplexed ImmunoSpot™ enables streamlined assessment of antigen-specific B cells; lessons toward maximizing cell utilization and increasing sample throughput

Abstract There are few techniques capable of detecting rare antigen-specific B cells while also providing information regarding their abundance, Ig class/subclass usage and functional affinity. The ImmunoSpot™ assay approach is suited for such antigen-specific B cell assessments since it provides information at single-cell resolution for individual ASC. Moreover, recently introduced innovations in the implementation of this assay modality have opened the door to testing larger sample sets. Towards this objective, multiplexed B cell FluoroSpot assays reduce the cell material requirement through parallel assessment of multiple Ig classes or IgG subclasses. Nevertheless, accurate determination of ASC frequencies, especially in the context of diverse antigen panels and complex exposure histories, is best achieved through evaluating multiple cell inputs to accommodate the inherent variability present within and amongst individual donors. The scope of this research effort was to further optimize the assay pipeline to facilitate high-throughput suitable assessment of antigen-specific ASC. This goal has been achieved through introducing advancements in the image analysis software component, improving both the time requirement and precision of downstream data analysis. Collectively, implementation of these assay optimizations serves to increase the feasibility of making high-throughput assessment of antigen-specific ASC using the ImmunoSpot™ approach a routine practice in immune monitoring.

Evaluation of in vitro bioaccessibility of Cu, Fe, Mn, and Zn from cooked Uruguayan pink shrimp by microwave induced plasma atomic emission spectrometry

Microwave induced plasma atomic emission spectrometry (MP-AES) was evaluated as a strategy for the analysis of simulated gastrointestinal solutions to estimate the in vitro bioaccessibility of essential elements in cooked pink shrimp. Operational conditions such as pump speed, nitrogen flow, and viewing position were thoroughly optimized for each element. Afterwards the validation of the analytical method was performed. Limits of quantification ranged from 0.005 mg kg−1 (Mn) to 0.106 mg kg−1 (Zn). Accuracy was evaluated by using a certified reference material and performing a mass-balance study. Suitable mass balances within the range 95–105% were obtained. In vitro bioaccessibility in cooked shrimp samples ranged from 14.7% (Fe) to 48.1% (Zn), in agreement with previous data from other shrimp species. The proposed procedure proved to be an outstanding sequential analytical strategy for elemental bioaccessibility studies, providing simplicity and high sample throughput compared to conventional approaches. Furthermore, this work constitutes the first work regarding the optimization of an elemental bioaccessibility study on animal protein employing MP-AES.

Rapid spectrophotometric detection for optimized production of landomycins and characterization of their therapeutic potential.

Microbial-derived natural products remain a major source of structurally diverse bioactive compounds and chemical scaffolds that have the potential as new therapeutics to target drug-resistant pathogens and cancers. In particular, genome mining has revealed the vast number of cryptic or low-yield biosynthetic gene clusters in the genus Streptomyces. However, low natural product yields-improvements to which have been hindered by the lack of high throughput methods-have slowed the discovery and development of many potential therapeutics. Here, we describe our efforts to improve yields of landomycins-angucycline family polyketides under investigation as cancer therapeutics-by a genetically modified Streptomyces cyanogenus 136. After simplifying the extraction process from S. cyanogenus cultures, we identified a wavelength at which the major landomycin products are absorbed in culture extracts, which we used to systematically explore culture medium compositions to improve total landomycin titers. Through correlational analysis, we simplified the culture optimization process by identifying an alternative wavelength at which culture supernatants absorb yet is representative of total landomycin titers. Using the subsequently improved sample throughput, we explored landomycin production during the culturing process to further increase landomycin yield and reduce culture time. Testing the antimicrobial activity of the isolated landomycins, we report broad inhibition of Gram-positive bacteria, inhibition of fungi by landomycinone, and broad landomycin resistance by Gram-negative bacteria that is likely mediated by the exclusion of landomycins by the bacterial membrane. Finally, the anticancer activity of the isolated landomycins against A549 lung carcinoma cells agrees with previous reports on other cell lines that glycan chain length correlates with activity. Given the prevalence of natural products produced by Streptomyces, as well as the light-absorbing moieties common to bioactive natural products and their metabolic precursors, our method is relevant to improving the yields of other natural products of interest.

Microplastic analysis in sediments of the Elbe River by electrostatic separation and differential scanning calorimetry

This study presents the most extensive investigation of microplastic (MP) contents in sediment from the Elbe River. We employed electrostatic separation (ES) and differential scanning calorimetry (DSC) to overcome limitations of sample throughput and time-consuming analysis. In total 43 sediment samples were collected using a Van-Veen grab. Subsequently, coarse materials (d10 > 100 μm) and fine materials (d10 ≤ 100 μm) were enriched using ES and density separation. DSC was utilized for MP identification and quantification, based on the phase-transition signals of eight different polymers. MP presence was detected in 25 samples, with successful quantification in 12 samples. The MP content in coarse material samples from shoreline areas ranged from 0.52 to 1.30 mg/kg, while in fine material samples from harbor basins, it ranged from 5.0 to 44.6 mg/kg. The most prevalent polymers identified were LD-PE, HD-PE, PP, and PCL. These findings confirmed the suitability of DSC for analyzing MP in complex environmental samples. MP hotspots were identified in harbor basins, where natural sedimentation processes and increased anthropogenic activities contribute to MP accumulation. Additionally, industrial sewage potentially contributed to MP content in sediment samples. The highest pollution levels were observed in the middle Elbe, between the confluences of Mulde and Havel. Lowest MP contents were found in the lower Elbe, potentially influenced by tides. Future studies should focus on holistic investigations of selected river sections, encompassing sediment, water, and biota samples, rather than the entire catchment area. This approach would facilitate the generation of spatiotemporal data on MP distribution in freshwater streams. In addition, more research is needed to explore potential interactions between different MP and sediment types during DSC measurements.

Functionalizing tandem mass tags for streamlining click-based quantitative chemoproteomics

Mapping the ligandability or potential druggability of all proteins in the human proteome is a central goal of mass spectrometry-based covalent chemoproteomics. Achieving this ambitious objective requires high throughput and high coverage sample preparation and liquid chromatography-tandem mass spectrometry analysis for hundreds to thousands of reactive compounds and chemical probes. Conducting chemoproteomic screens at this scale benefits from technical innovations that achieve increased sample throughput. Here we realize this vision by establishing the silane-based cleavable linkers for isotopically-labeled proteomics-tandem mass tag (sCIP-TMT) proteomic platform, which is distinguished by early sample pooling that increases sample preparation throughput. sCIP-TMT pairs a custom click-compatible sCIP capture reagent that is readily functionalized in high yield with commercially available TMT reagents. Synthesis and benchmarking of a 10-plex set of sCIP-TMT reveal a substantial decrease in sample preparation time together with high coverage and high accuracy quantification. By screening a focused set of four cysteine-reactive electrophiles, we demonstrate the utility of sCIP-TMT for chemoproteomic target hunting, identifying 789 total liganded cysteines. Distinguished by its compatibility with established enrichment and quantification protocols, we expect sCIP-TMT will readily translate to a wide range of covalent chemoproteomic applications.

Inserting Pre-analytical Chromatographic Priming Runs Significantly Improves Targeted Pathway Proteomics with Sample Multiplexing.

GoDig, a platform for targeted pathway proteomics without the need for manual assay scheduling or synthetic standards, is a powerful, flexible, and easy-to-use method that uses tandem mass tags to increase sample throughput up to 18-fold relative to label-free methods. Though the protein-level success rates of GoDig are high, the peptide-level success rates are more limited, hampering assays of harder-to-quantify proteins and site-specific phenomena. To guide the optimization of GoDig assays as well as improvements to the GoDig platform, we created GoDigViewer, a new stand-alone software that provides detailed visualizations of GoDig runs. GoDigViewer guided the implementation of "priming runs," an acquisition mode with significantly higher success rates. In this mode, two or more chromatographic priming runs are automatically performed to improve the accuracy and precision of target elution orders, followed by analytical runs which quantify targets. Using priming runs, success rates exceeded 97% for a list of 400 peptide targets and 95% for a list of 200 targets that are usually not quantified using untargeted mass spectrometry. We used priming runs to establish a quantitative assay of 125 macroautophagy proteins that had a >95% success rate and revealed differences in macroautophagy expression profiles across four human cell lines.

Gold leaf electrochemical flow cell for determination of iodide in nuclear emergency tablets

This work introduces an innovative gold-leaf flow cell for electrochemical detection in flow injection (FI) analysis. The flow cell incorporates a hammered custom gold leaf electrochemical sensor. Hammered gold leaves consist of pure gold and are readily available in Thailand at affordable prices (approximately $0.085 for a sheet measuring 40 mm × 40 mm). Four sensing devices can be made from a single sheet of this gold leaf, resulting in a production cost of approximately $0.19 per sensor. Each electrochemical sensor has the gold leaf as the working electrode, together with a printed carbon strip, and a printed silver/silver chloride strip as the counter and reference electrodes, respectively. Initial investigations using cyclic voltammetry of a standard 1000 μmol L⁻1 iodide solution in 60 mmol L⁻1 phosphate buffer (PB) solution at pH 5, demonstrated performance comparable to that of a commercial screen-printed gold electrode. The hammered gold leaf electrode was then installed in a commercial flow cell as part of an FI system. A sample or standard iodide solution (100 μL) is injected into the first carrier stream of phosphate buffer (PB) solution, which then merges to mix with the second stream of the same buffer solution before flowing into the flow cell for amperometric detection of iodide. The optimized operating conditions include a fixed potential of +0.39 V (vs Ag/AgCl), and a total flow rate of 3 mL min⁻1. A linear calibration is obtained in the concentration range of 1 to 1000 μmol L⁻1 I− with a typical equation of μA = (0.00299 ± 0.00004) × (μmol L−1 I−) + (0.021 ± 0.020), and R2 = 0.9994. Analysis of iodide using this gold leaf-FI system is rapid with sample throughput of 86 samples h⁻1 and %RSD of a sample of 100 μmol L⁻1 I⁻ of 1.2 (n = 29). The limit of detection, (calculated as 2.78 × SD of regression line/slope), is 27 μmol L⁻1 I−. This method was successfully applied to determine iodide in nuclear emergency tablets.

Methodology for high-performance liquid chromatography detection of latanoprost and latanoprost free acid

AbstractA gradient high-performance liquid chromatography (HPLC) method has been developed to determine the concentrations of latanoprost (LP) and latanoprost free acid (LPA) in aqueous solutions. It is novel due to a combination of its simplicity, speed, and detection capability in aqueous solutions for both active drug (LPA) and prodrug (LP). This method is applicable for the research and development of novel drug delivery devices and quality control assays for experimental and commercial laboratory settings, as it allows for a high sample throughput. Samples were chromatographed across a C18 + 2.7 µm 4.6 × 7.5 mm reversed-phase column with gradient elution using a mobile phase of aqueous acetic acid (pH 3.1) and acetonitrile with 0.1% acetic acid. UV spectrophotometry was used to monitor the eluents at 210 nm. Drug concentrations from 1.0 to 150 μg mL−1 were tested, with good linearity observed across the range. LPA had a signature peak at approximately 4.82 min (SD < 0.08) and LP at 9.27 min (SD < 0.07). For both drug and pro-drug, LOD and LOQ were 1.0 and 2.5 μg mL−1, respectively. This assay which accurately measures both prodrug and drug in a single injection, has significant applicability in determining the release kinetics of novel LP drug delivery systems.

Atomic-Scale Characterization of Microscale Battery Particles Enabled by a High-Throughput Focused Ion Beam Milling Technique.

The cathode materials in lithium-ion batteries (LIBs) require improvements to address issues such as surface degradation, short-circuiting, and the formation of dendrites. One such method for addressing these issues is using surface coatings. Coatings can be sought to improve the durability of cathode materials, but the characterization of the uniformity and stability of the coating is important to assess the performance and lifetime of these materials. For microscale particles, there are, however, challenges associated with characterizing their surface modifications by transmission electron microscopy (TEM) techniques due to the size of these particles. Often, techniques such as focused ion beam (FIB)-assisted lift-out can be used to prepare thin cross sections to enable TEM analysis, but these techniques are very time-consuming and have a relatively low throughput. The work outlined herein demonstrates a FIB technique with direct support of microscale cathode materials on a TEM grid that increases sample throughput and reduces the processing time by 60-80% (i.e., from >5 to ∼1.5 h). The demonstrated workflow incorporates an air-liquid particle assembly followed by direct particle transfer to a TEM grid, FIB milling, and subsequent TEM analysis, which was illustrated with lithium nickel cobalt aluminum oxide particles and lithium manganese nickel oxide particles. These TEM analyses included mapping the elemental composition of cross sections of the microscale particles using energy-dispersive X-ray spectroscopy. The methods developed in this study can be extended to high-throughput characterization of additional LIB cathode materials (e.g., new compositions, coating, end-of-life studies), as well as to other microparticles and their coatings as prepared for a variety of applications.

Comprehensive Prostate Fluid-Based Spectral Libraries for Enhanced Protein Detection in Urine.

Biofluids contain molecules in circulation and from nearby organs that can be indicative of disease states. Characterizing the proteome of biofluids with DIA-MS is an emerging area of interest for biomarker discovery; yet, there is limited consensus on DIA-MS data analysis approaches for analyzing large numbers of biofluids. To evaluate various DIA-MS workflows, we collected urine from a clinically heterogeneous cohort of prostate cancer patients and acquired data in DDA and DIA scan modes. We then searched the DIA data against urine spectral libraries generated using common library generation approaches or a library-free method. We show that DIA-MS doubles the sample throughput compared to standard DDA-MS with minimal losses to peptide detection. We further demonstrate that using a sample-specific spectral library generated from individual urines maximizes peptide detection compared to a library-free approach, a pan-human library, or libraries generated from pooled, fractionated urines. Adding urine subproteomes, such as the urinary extracellular vesicular proteome, to the urine spectral library further improves the detection of prostate proteins in unfractionated urine. Altogether, we present an optimized DIA-MS workflow and provide several high-quality, comprehensive prostate cancer urine spectral libraries that can streamline future biomarker discovery studies of prostate cancer using DIA-MS.

High-throughput DNA extraction and cost-effective miniaturized metagenome and amplicon library preparation of soil samples for DNA sequencing.

Reductions in sequencing costs have enabled widespread use of shotgun metagenomics and amplicon sequencing, which have drastically improved our understanding of the microbial world. However, large sequencing projects are now hampered by the cost of library preparation and low sample throughput, comparatively to the actual sequencing costs. Here, we benchmarked three high-throughput DNA extraction methods: ZymoBIOMICS™ 96 MagBead DNA Kit, MP BiomedicalsTM FastDNATM-96 Soil Microbe DNA Kit, and DNeasy® 96 PowerSoil® Pro QIAcube® HT Kit. The DNA extractions were evaluated based on length, quality, quantity, and the observed microbial community across five diverse soil types. DNA extraction of all soil types was successful for all kits, however DNeasy® 96 PowerSoil® Pro QIAcube® HT Kit excelled across all performance parameters. We further used the nanoliter dispensing system I.DOT One to miniaturize Illumina amplicon and metagenomic library preparation volumes by a factor of 5 and 10, respectively, with no significant impact on the observed microbial communities. With these protocols, DNA extraction, metagenomic, or amplicon library preparation for one 96-well plate are approx. 3, 5, and 6 hours, respectively. Furthermore, the miniaturization of amplicon and metagenome library preparation reduces the chemical and plastic costs from 5.0 to 3.6 and 59 to 7.3 USD pr. sample. This enhanced efficiency and cost-effectiveness will enable researchers to undertake studies with greater sample sizes and diversity, thereby providing a richer, more detailed view of microbial communities and their dynamics.

Comparative Analysis of Single-Cell RNA Sequencing Methods with and without Sample Multiplexing.

Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique for investigating biological heterogeneity at the single-cell level in human systems and model organisms. Recent advances in scRNA-seq have enabled the pooling of cells from multiple samples into single libraries, thereby increasing sample throughput while reducing technical batch effects, library preparation time, and the overall cost. However, a comparative analysis of scRNA-seq methods with and without sample multiplexing is lacking. In this study, we benchmarked methods from two representative platforms: Parse Biosciences (Parse; with sample multiplexing) and 10x Genomics (10x; without sample multiplexing). By using peripheral blood mononuclear cells (PBMCs) obtained from two healthy individuals, we demonstrate that demultiplexed scRNA-seq data obtained from Parse showed similar cell type frequencies compared to 10x data where samples were not multiplexed. Despite relatively lower cell capture affecting library preparation, Parse can detect rare cell types (e.g., plasmablasts and dendritic cells) which is likely due to its relatively higher sensitivity in gene detection. Moreover, a comparative analysis of transcript quantification between the two platforms revealed platform-specific distributions of gene length and GC content. These results offer guidance for researchers in designing high-throughput scRNA-seq studies.

An integrated method for rapid extraction of fluorescent whitening agents from selected cosmetics by in situ formation of deep eutectic solvent

A novel extraction methodology was developed based on deep eutectic solvent (DES) in situ formation. The solvent was synthesized from a binary mixture of L-cysteine, functioning as a hydrogen bond acceptor, and 2-methylphenol, serving as a hydrogen bond donor. The DES’s inherent molecular structures and extensive hydrogen bonding networks were characterized using the Fourier-transform infrared spectroscopy (FT-IR), while its hydrophobic nature was assessed by determining molecular polarity. Its extraction efficiency was demonstrated through the extraction of fluorescent whitening agents (FWAs) in cosmetic products, acting as a model analytical application. This was accomplished using vortex-assisted emulsification solid–liquid extraction (SLE) method, followed by high-performance liquid chromatography-fluorescence detection. Response surface methodology was employed to optimize extraction conditions in a multivariate experimental design. This approach streamlined the multi-operation extraction process via ingeniously integrating extraction and clean-up into a single step, resulting in significant reductions in extraction time required and high sample throughputs of approximately 40 samples per hour. The methodology was validated and exhibited excellent linearity in concentration ranges of 0.01–24 mg/L for five FWAs and 0.01–40 mg/L for other three FWAs, with correlation coefficients (r) ranging from 0.9985 to 1.000. The limits of detection and quantification were in the range of 0.03–0.26 mg kg−1 and 0.10–0.87 mg kg−1, respectively. The reliability and practicality of the proposed method were affirmed by quantifying eight FWAs in ninety-four commercially available facial masks and whitening creams, yielding recoveries values between 90.0 % and 106.0 % with relative standard deviations (RSDs) of 1.0–4.3 %. Inorganic ions and organic compounds present in the samples had minimal impact on FWAs detection following sample pre-treatment. This procedure showcased exceptional extraction capabilities towards a diverse array of FWAs with the aid of multiple interactions, suggesting significant potential for increasing sample throughput while reducing organic solvent and material consumptions compared with conventional SLE methods. The low-toxicity DES is an excellent alternative to traditional extractants typically applied to SLE techniques.

High throughput application of ASTM D8332: Detailed prototype design and operating conditions for microplastic sampling of riverine systems

Microplastic sampling strategies for aquatic systems commonly employ small mesh nets to collect suspended microparticles. These methods work well for marine sampling campaigns; however, complex water systems such as freshwater rivers, effluent discharges, and stormwater ponds characterized by high total suspended solids and fast-moving water can cause the nets to clog, rip, or tear. Published in 2020, ASTM D8332 is an alternative approach to sampling complex water systems for microplastics involving pumping large volumes of water across a cascading stack of sieves to collect suspended particles. Here we show that ASTM D8332 can be applied to sample freshwater rivers for microplastic collection. A high throughput sampling prototype developed in this work is capable of pumping 1500 L of river water in 45 min to collect particles as small as 45 µm. The system is lightweight, modular, and easily transportable. It has a discrete power supply, allowing for the collection of microplastics anywhere along the river, including municipal discharges. The design minimizes the amount of plastic in the flow path and provides a practical way to measure field contamination. Finally, we outline lessons learned through extensive field trials and testing using this system sampling the North Saskatchewan River in Edmonton, Alberta.•Existing small mesh nets face limitations in freshwater rivers, encountering clogging and tearing issues from high suspended solids and fast moving water.•Using a standardized method, ASTM D8332 - a pumping-based approach is efficient for microplastic collection in freshwater rivers.•Lightweight, modular, plastic free prototype system pumps 1500 L of river water in 45 min, collecting particles as small as 45 µm. Successfully tested in the North Saskatchewan River.

Improving Autonomous Separation Assurance through Distributed Reinforcement Learning with Attention Networks

Advanced Air Mobility (AAM) introduces a new, efficient mode of transportation with the use of vehicle autonomy and electrified aircraft to provide increasingly autonomous transportation between previously underserved markets. Safe and efficient navigation of low altitude aircraft through highly dense environments requires the integration of a multitude of complex observations, such as surveillance, knowledge of vehicle dynamics, and weather. The processing and reasoning on these observations pose challenges due to the various sources of uncertainty in the information while ensuring cooperation with a variable number of aircraft in the airspace. These challenges coupled with the requirement to make safety-critical decisions in real-time rule out the use of conventional separation assurance techniques. We present a decentralized reinforcement learning framework to provide autonomous self-separation capabilities within AAM corridors with the use of speed and vertical maneuvers. The problem is formulated as a Markov Decision Process and solved by developing a novel extension to the sample-efficient, off-policy soft actor-critic (SAC) algorithm. We introduce the use of attention networks for variable-length observation processing and a distributed computing architecture to achieve high training sample throughput as compared to existing approaches. A comprehensive numerical study shows that the proposed framework can ensure safe and efficient separation of aircraft in high density, dynamic environments with various sources of uncertainty.

Abstract 320: Development and automation of a streamlined targeted enrichment method for cancer mutation detection

Abstract Next Generation Sequencing (NGS) of DNA is a powerful tool for the detection of genetic variations, including single nucleotide polymorphisms, copy number variation, and small insertions/deletions. Target enrichment technologies enhance DNA sequencing by enabling users to analyze specific regions of interest only, which helps to effectively increase sequencing depth and sample throughput while minimizing cost. However, many targeted DNA library construction workflows are not optimal for routine genetic testing needs due to inconsistent, lengthy workflow. This poses significant challenge to application like cancer mutation profiling that requires detection sensitivity down to 1% or below due to heterogeneous nature of tumor tissue. In addition, high throughput testing with minimal hands on time is desirable with the rapid advance of precision medicine. Magnetic bead separations are commonly used between the individual reactions of targeted DNA library preparation workflows for cleanup and size selection. These bead clean up reactions are not only labor-intensive and tedious procedures but can also greatly contribute to sample-to sample variation especially when employing automated library preparation procedures. With the sophisticated QIAseq Targeted DNA Pro, we developed a novel streamlined targeted DNA workflow that greatly reduces handling variation by replacing the majority of bead clean up steps with enzymatic reactions, which now can be finished in as little as six hours. In combination with the newly developed QIAseq Normalizer kit, the protocol has been successfully implemented on the Hamilton NGS Star liquid handling platform resulting in up to 96 highly uniform, complex and ready-to-sequence libraries that can be effortless generated in one run. This complete automated solution saves researcher up to four hours of hands-on time. When using commercial reference samples, cancer mutations down to 1% were consistently detected with this automated workflow. The presented data demonstrate that this integrated and streamlined workflow does not only provide an automation friendly workflow but also allows to reliably identify low frequent cancer mutations. The applications presented here are for research use only. Not for use in diagnostic procedures. Citation Format: Zhong Wu, Michelle Baird, Cornelia Mechlen, Peter Hahn, Jonathan M. Shaffer. Development and automation of a streamlined targeted enrichment method for cancer mutation detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 320.

Mass Spectrometry-Compatible Elution Technique Enables an Improved Mucin-Selective Enrichment Strategy to Probe the Mucinome.

Mucin-domain glycoproteins are densely O-glycosylated and play critical roles in a host of healthy and disease-driven biological functions. Previously, we developed a mucin-selective enrichment strategy by employing a catalytically inactive mucinase (StcE) conjugated to a solid support. While this method was effective, it suffered from low throughput and high sample requirements. Further, the elution step required boiling in SDS, thus necessitating an in-gel digest with trypsin. Here, we introduce innovative elution conditions amenable to mucinase digestion and downstream analysis using mass spectrometry. This increased throughput and lowered sample input while maintaining mucin selectivity and enhancing the glycopeptide signal. We then benchmarked this technique against different O-glycan binding moieties for their ability to enrich mucins from various cell lines and human serum. Overall, the new method outperformed our previous procedure and all of the other enrichment techniques tested. This allowed for the effective isolation of more mucin-domain glycoproteins, resulting in a high number of O-glycopeptides, thus enhancing our ability to analyze the mucinome.

Development of a robust cell-based potency assay for a coxsackievirus A21 oncolytic virotherapy

Oncolytic viruses (OV) are part of a burgeoning field of investigational oncolytic therapy (OT), in which lytic viruses dissolve advanced tumors productively and specifically. One such OT is a Coxsackievirus A21 (CVA21) based OV that is currently under clinical evaluation. A tissue culture infectious dose (TCID50) assay was used for CVA21 potency release and stability testing in early clinical development. The titer measured in this method was an extrapolated value from cytopathic effect (CPE) observed during the serial dilution but doesn't represent direct viral killing of cells. Moreover, the assay was not deemed to be optimal to carry into late phase clinical development due to limitations in assay precision, turn-around time, and sample throughput. To address these points, we developed a plaque assay to measure viral plaque forming units to measure the potency value for drug substance (DS), drug product (DP) and virus seed (master and working) stocks. In this manuscript, we describe the steps taken to develop this plaque assay for the late-stage clinical development, which include the assay qualification, validation, and robustness protocols, and describe statistical methods for data analysis. Moreover, the method was validated for linearity, accuracy, precision, and specificity. Furthermore, the plaque assay quantifies OV infectivity with better precision (32% vs 58%), with higher sample throughput (22 samples/week vs 3 samples/week) and shorter assay turnaround time (4 days vs 7 days) than the TCID50 method. This assay development strategy can provide guidance for the development of robust cell-based potency methods for OVs and other infectious viral products.

Quantitative Analysis of NDMA in Drug Products: A Proposed High-Throughput Approach Using Headspace–SIFT-MS

Since the initial 2018 recall of angiotensin receptor blockers due to unacceptable levels of mutagenic N-nitrosodimethylamine (NDMA) impurity, numerous drug products delivering diverse active pharmaceutical ingredients (APIs) have been recalled. Regulators and the industry are working together to understand and address this widescale problem. Conventional analysis of NDMA utilizes liquid or gas chromatography-based procedures that can involve complicated sample preparation and slow sample analysis. Selected ion flow tube mass spectrometry (SIFT-MS) analyses NDMA directly in the gas phase using soft chemical ionization, with an LOQ of 2 ng g−1. Through the novel application of the multiple headspace extraction (MHE) technique, NDMA was quantified directly and rapidly from the drug product without dissolution, at levels well below the regulatory acceptable intake of 96 ng day−1. A comparative analysis of recalled metformin using MHE-SIFT-MS and a conventional liquid chromatography–mass spectrometry/mass spectrometry (LC-MS/MS) method showed good agreement. Use of the novel MHE-SIFT-MS approach may enable a wider screening of drug products to be conducted, since it provides around a three-fold increase in daily sample throughput.

A dual-reference study design for understanding and improving AAV genome size analysis.

Recombinant adeno-associated virus (rAAV) is the leading platform of gene delivery for its long-lasting gene transformation and low immunogenicity. Characterization of the integrity and purity of the rAAV genome is critical to ensure clinical potency and safety. However, current rAAV genome characterization methods that can provide size assessment are either time-consuming or not easily accessible to general labs. Additionally, there is a lack of right reference standard for analyzing long single-stranded DNA (ssDNA) fragments. Here, we have developed an ssDNA assay on a microfluidic capillary electrophoresis platform using ssDNA reference standard. This assay provides size calling for ssDNA fragment, a detection sensitivity at ∼89pg/µL (3×1010GC/mL AAV) for 5.1kb ssDNA fragment, and a turnaround time at ∼100s per sample with a high throughput sample analyzing capability. Moreover, we have observed that the annealing of AAV ssDNA subsequent to its release from the capsid might introduce an additional double-stranded DNA (dsDNA) peak. This phenomenon is dependent on the sample processing workflow. To avoid the risk of mischaracterization, we recommend the use of dual-reference standards in combination with other orthogonal methods to have a comprehensive understanding of the rAAV genome size and integrity.