Multiple Assays Research Articles

An Update on the Current State of SARS-CoV-2 Mac1 Inhibitors.

Non-structural protein 3 (nsp3) from all coronaviruses (CoVs) contains a conserved macrodomain, known as Mac1, that has been proposed as a potential therapeutic target for CoVs due to its critical role in viral pathogenesis. Mac1 is an ADP-ribose binding protein and ADP-ribosylhydrolase that promotes replication and blocks IFN responses, though the precise mechanisms it uses to carry out these functions remain unknown. Over the past 3 years following the onset of COVID-19, several groups have used high-throughput screening with multiple assays and chemical modifications to create unique chemical inhibitors of the SARS-CoV-2 Mac1 protein. Here, we summarize the current efforts to identify selective and potent inhibitors of SARS-CoV-2 Mac1.

Improved performance of nucleic acid-based assays for genetically diverse norovirus surveillance.

Nucleic acid-based assays, such as polymerase chain reaction (PCR), that amplify and detect organism-specific genome sequences are a standard method for infectious disease surveillance. However, challenges arise for virus surveillance because of their genetic diversity. Here, we calculated the variability of nucleotides within the genomes of 10 human viral species in silico and found that endemic viruses exhibit a high percentage of variable nucleotides (e.g., 51.4% for norovirus genogroup II). This genetic diversity led to the variable probability of detection of PCR assays (the proportion of viral sequences that contain the assay's target sequences divided by the total number of viral sequences). We then experimentally confirmed that the probability of the target sequence detection is indicative of the number of mismatches between PCR assays and norovirus genomes. Next, we developed a degenerate PCR assay that detects 97% of known norovirus genogroup II genome sequences and recognized norovirus in eight clinical samples. By contrast, previously developed assays with 31% and 16% probability of detection had 1.1 and 2.5 mismatches on average, respectively, which negatively impacted RNA quantification. In addition, the two PCR assays with a lower probability of detection also resulted in false negatives for wastewater-based epidemiology. Our findings suggest that the probability of detection serves as a simple metric for evaluating nucleic acid-based assays for genetically diverse virus surveillance. IMPORTANCE Nucleic acid-based assays, such as polymerase chain reaction (PCR), that amplify and detect organism-specific genome sequences are employed widely as a standard method for infectious disease surveillance. However, challenges arise for virus surveillance because of the rapid evolution and genetic variation of viruses. The study analyzed clinical and wastewater samples using multiple PCR assays and found significant performance variation among the PCR assays for genetically diverse norovirus surveillance. This finding suggests that some PCR assays may miss detecting certain virus strains, leading to a compromise in detection sensitivity. To address this issue, we propose a metric called the probability of detection, which can be simply calculated in silico using a code developed in this study, to evaluate nucleic acid-based assays for genetically diverse virus surveillance. This new approach can help improve the sensitivity and accuracy of virus detection, which is crucial for effective infectious disease surveillance and control.

Droplet digital PCR: A comprehensive tool for genetic analysis and prediction of bispecific antibody assembly during cell line development

Molecular biological methods have emerged as inevitable tools to accompany the process of cell line development for the generation of stable and highly productive manufacturing cell lines in the biopharmaceutical industry. PCR-based methods are especially useful for screening and characterization of cell lines due to their low cost, scalability, precision and propensity for multidimensional read-outs. In this study, the diverse applications of droplet digital PCR (ddPCR) as a molecular biological tool for cell line development are demonstrated. Specifically, it is shown that ddPCR can be used to enable precise, sensitive and reproducible absolute quantification of genomically integrated transgene copies during cell line development and cell bank characterization. Additionally, an amplitude multiplexing approach is applied to simultaneously run multiple assays on different genetic targets in a single reaction and advance clonal screening by measuring gene expression profiles to predict the assembly and homogeneity of difficult-to-express (DTE) proteins. The implementation of ddPCR-based assays during cell line development allows for early screening at a transcriptional level, particularly for complex, multidomain proteins, where balanced polypeptide chain ratios are of primary importance. Moreover, it is demonstrated that ddPCR-based genomic characterization improves the robustness, efficiency and comparability of absolute transgene copy number quantification, an essential genetic parameter that must be demonstrated to regulatory authorities during clinical trial and market authorization application submissions to support genetic stability and consistency of the selected cell substrate.

The Evaluation of Clot Waveform Analyses for Assessing Hypercoagulability in Patients Treated with Factor VIII Concentrate.

Regular prophylactic therapy has become an increasingly common treatment for severe hemophilia. Therefore, hypercoagulability-a potential risk factor of thrombosis-is a cause for concern in hemophilic patients treated with a high dose of FVIII concentrate. In clot waveform analysis (CWA)-thrombin time (TT), a small amount of thrombin activates clotting factor VIII (FVIII) instead of fibrinogen, resulting in FVIII measurements using CWA-TT with a small amount of thrombin. The coagulation ability of patients treated with FVIII concentrate or emicizumab was evaluated using activated partial thromboplastin time (APTT), TT and a small amount of tissue factor-induced FIX activation assay (sTF/FIXa) using CWA. The FVIII activity based on CWA-TT was significantly greater than that based on the CWA-APTT or chromogenic assay. FVIII or FVIII-like activities based on the three assays in plasma without emicizumab were closely correlated; those in plasma with emicizumab based on CWA-TT and chromogenic assays were also closely correlated. CWA-APTT and CWA-TT showed different patterns in patients treated with FVIII concentrates compared to those treated with emicizumab. In particular, CWA-TT in patients treated with FVIII concentrate showed markedly higher peaks in platelet-rich plasma than in platelet-poor plasma. CWA-APTT showed lower coagulability in hemophilic patients treated with FVIII concentrate than in healthy volunteers, whereas CWA-sTF/FIXa did not. In contrast, CWA-TT showed hypercoagulability in hemophilic patients treated with FVIII concentrate. CWA-TT can be used to evaluate the thrombin bursts that cause hypercoagulability in patients treated with emicizumab. Although routine APTT evaluations demonstrated low coagulation ability in patients treated with FVIII concentrate, CWA-TT showed hypercoagulability in these patients, suggesting that the evaluation of coagulation ability may be useful when using multiple assays.

Ruangan Lidan decoction inhibits the growth and metastasis of liver cancer by downregulating miR-9-5p and upregulating PDK4

ABSTRACT A growing number of studies have suggested that traditional Chinese medicine (TCM) plays an essential role in the development and occurrence of liver cancer. However, the function of Ruangan Lidan decoction (RLD) in liver cancer are not yet adequately identified and manifested, which attracted our attention. The key genes related to liver cancer and RLD and the upstream miRNAs of PDK4 were obtained based on bioinformatics analysis, followed by verification of the targeting relationship between miR-9-5p and PDK4. Next, Huh7 cells were treated with RLD to detect cell proliferation, colony formation, migration, invasion, and apoptosis by multiple assays with gain- and loss-of-function experiments. Moreover, subcutaneous transplanted tumor model and lung metastasis model of liver cancer in nude mice were established to further verify the functional role of RLD in liver cancer growth and metastasis via miR-9-5p/PDK4 axis. Bioinformatics analysis found that PDK4 and miR-9-5p were related to liver cancer, and PDK4 may be a downstream regulator of RLD. miR-9-5p could target and inhibit PDK4. In vitro cell experiments demonstrated that RLD suppressed liver cancer cell proliferation, invasion and migration, and promoted apoptosis by inhibiting miR-9-5p expression and promoting PDK4 expression. In vivo animal experiments further confirmed that RLD inhibited liver cancer growth and metastasis via upregulation of miR-9-5p-dependent PDK4. RLD downregulated miR-9-5p and upregulated PDK4 to inhibit the proliferation, migration, invasion, and induce apoptosis, thereby suppressing the growth and metastasis of liver cancer, highlighting a potential novel target for treatment of liver cancer.

Novel spirooxindole alkaloid derivatives from the medicinal insect Blaps japanensis and their biological evaluation

Blapspirooxindoles A–C (1–3), three novel spirooxindole alkaloids with a unique spiro[chromane-4,3′-indoline]-2,2′-dione motif, blapcumaranons A and B (4 and 5), two new 2-cumaranon derivatives, blapoxindoles A–J (6–15), ten new oxindole alkaloid derivatives, along with one known compound (16), were isolated from the whole bodies of Blaps japanensis. Their structures including absolute configurations were determined by using spectroscopic, X-ray crystallographic, and computational methods. Compounds 1–11 and 13 exist as racemic mixtures in nature, and their (–)- and (+)-antipodes were separated by chiral HPLC. Biological evaluations of these compounds were determined with multiple assays including anti-tumor, anti-inflammatory, and renal protection activities in vitro. Several compounds displayed effective activity in one or more assays.

CovidShiny: An Integrated Web Tool for SARS-CoV-2 Mutation Profiling and Molecular Diagnosis Assay Evaluation In Silico.

The coronavirus disease 2019 (COVID-19) pandemic is still ongoing, with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continuing to evolve and accumulate mutations. While various bioinformatics tools have been developed for SARS-CoV-2, a well-curated mutation-tracking database integrated with in silico evaluation for molecular diagnostic assays is currently unavailable. To address this, we introduce CovidShiny, a web tool that integrates mutation profiling, in silico evaluation, and data download capabilities for genomic sequence-based SARS-CoV-2 assays and data download. It offers a feasible framework for surveilling the mutation of SARS-CoV-2 and evaluating the coverage of the molecular diagnostic assay for SARS-CoV-2. With CovidShiny, we examined the dynamic mutation pattern of SARS-CoV-2 and evaluated the coverage of commonly used assays on a large scale. Based on our in silico analysis, we stress the importance of using multiple target molecular diagnostic assays for SARS-CoV-2 to avoid potential false-negative results caused by viral mutations. Overall, CovidShiny is a valuable tool for SARS-CoV-2 mutation surveillance and in silico assay design and evaluation.

The behavioral response to the putative necromones from dead Tribolium castaneum (Coleoptera: Tenebrionidae) in traps by conspecifics as a function of density and time since capture.

Long-term trapping programs of stored product pests provide information for timely and accurate pest management. Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae) is a highly successful external-infesting grain pest and is frequently monitored using a commercial pitfall trap that combines pheromonal and kairomonal stimuli. However, an often overlooked component of lure-based traps is the potential for the volatile plume to change over time as individuals are captured. These now-dead insects may then release necromones altering the captures of conspecifics. In this study, we evaluated changes in (i) the behavior of T. castaneum and (ii) the relative change in volatiles over time since dead insects were added and among different densities of dead conspecifics in a commercially available kairomone oil. We used multiple behavior assays, including wind tunnel, release-recapture, and 2-way olfactometer, and performed chemical analyses via headspace collection and gas chromatography coupled with mass spectrometry. Tribolium castaneum response to the kairomone lure was not consistent among assays of density of conspecifics between 4 and 40 adults after 24 or 96 h, or time of seeding over 1-96 h or 8-11 days prior. Tested strains collected in 2012 and 2019 ruled out strain-specific differences. Oil batch effects were also ruled out as a factor contributing to the response of T. castaneum. The relative volatile composition was generally stable among the treatments despite using different seeding densities and seeding times. Given that attraction and relative volatile composition were generally unaffected by prior captures, long-term monitoring programs may be robust in their interpretability over time.

Estrogenic activity of fermented soymilk extracts and soy compounds

To understand the complex mechanism of estrogen action, multiple assays based on different biological principles are necessary. The estrogenic activity of soymilk extracts was evaluated for soymilk extracts before and after fermentation using Lactobacillus delbrueckii, and the data were compared with major isoflavone constituents. Cell, protein, and transcription assays were used in this study to evaluate the estrogenic activity of soymilk extracts before and after fermentation, in addition to the activity of four soy compounds, namely genistein and daidzein and their glycosides, genistin and daidzin. These assays clearly demonstrated the estrogenic activity of these soymilk extracts and soy compounds, although the presence of complex mechanisms for the responses at the transcription level, presumably due to the differences in the mechanism of estrogen signaling. Furthermore, greater estrogenic activity was observed after fermentation of the soymilk extracts. The data obtained by RNA-sequencing were further examined using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases to determine cell functions, i.e., biological processes and metabolic pathways. Among the identified cell functions, the sets of genes for cell division/cell cycle and DNA replication/DNA repair were significantly up-regulated, whereas those for autophagy were significantly down-regulated, which explains the enhanced cell proliferation promoted by these materials. The estrogenic activity of soymilk extracts and soy flavonoids, and the contribution of fermentation, have multiple pharmacological benefits, including bone protection/bone regeneration, cancer chemoprevention, neuroprotection, and the treatment of menopausal syndromes.

Developmental validation of a novel multiple genotyping assay with 24 Canine STR loci

Canine individual identification and parentage testing are essential in various fields, including forensics and breeding programs. This study aimed to develop and validate the Canine 25 A kit, a multiplex polymerase chain reaction (PCR) system designed to address these critical requirements. This novel system enables the simultaneous amplification of 24 canine autosomal short tandem repeat (STR) loci and one sex-determining marker. Validation of the Canine 25 A kit was conducted following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines, demonstrating significant sensitivity, high inhibitor tolerance, canine specificity within a mixture, species specificity, and precision in genotype determination. The Canine 25 A kit was crucial in resolving several forensic cases, such as casework samples from a dog attack incident and parentage determination. Its effectiveness in genotyping these samples highlights its significance in forensic applications. Population genetic parameter analysis revealed a high discriminatory power, as indicated by the calculated combined discrimination power (CDP) values for each breed exceeding 0.999 999 999 999, while the combined power of exclusion (CPE) surpassed 0.9999. Overall, the Canine 25 A kit offers a precise and dependable tool for canine individual identification and parentage determination.

Small molecule activators of TAK1 promotes its activity-dependent ubiquitination and TRAIL-mediated tumor cell death

TAK1 is a key modulator of both NF-κB signaling and RIPK1. In TNF signaling pathway, activation of TAK1 directly mediates the phosphorylation of IKK complex and RIPK1. In a search for small molecule activators of RIPK1-mediated necroptosis, we found R406/R788, two small molecule analogs that could promote sustained activation of TAK1. Treatment with R406 sensitized cells to TNF-mediated necroptosis and RIPK1-dependent apoptosis by promoting sustained RIPK1 activation. Using click chemistry and multiple biochemical binding assays, we showed that treatment with R406 promotes the activation of TAK1 by directly binding to TAK1, independent of its original target Syk kinase. Treatment with R406 promoted the ubiquitination of TAK1 and the interaction of activated TAK1 with ubiquitinated RIPK1. Finally, we showed that R406/R788 could promote the cancer-killing activities of TRAIL in vitro and in mouse models. Our studies demonstrate the possibility of developing small molecule TAK1 activators to potentiate the effect of TRAIL as anticancer therapies.

Examining the oxidative potential of residential outdoor PM2.5 through multiple assays and their potential chemical drivers

Examining the oxidative potential of residential outdoor PM2.5 through multiple assays and their potential chemical drivers

Molecular neuropathology: an essential and evolving toolbox for the diagnosis and clinical management of central nervous system tumors.

Molecular profiling has transformed the diagnostic workflow of CNS tumors during the last years. The latest WHO classification of CNS tumors (5th edition), published in 2021, pushed forward the integration between histopathological features and molecular hallmarks to achieve reproducible and clinically relevant diagnoses. To address these demands, pathologists have to appropriately deal with multiple molecular assays mainly including DNA methylation profiling and DNA/RNA next generation sequencing. Tumor classification by DNA methylation profiling is now a critical tool for many diagnostic tasks in neuropathology including the assessment of complex cases, to evaluate novel tumor types and to perform tumor subgrouping in hetereogenous entities like medulloblastoma or ependymoma. DNA/RNA NGS allow the detection of multiple molecular alterations including single nucleotide variations, small insertions/deletions (InDel), and gene fusions. These molecular markers can provide key insights for diagnosis, for example, if a tumor-specific mutation is detected, but also for treatment since targeted therapies are progressively entering the clinical practice. In the present review, a brief, but comprehensive overview of these tools will be provided, discussing their technical specifications, diagnostic value, and potential limitations. Moreover, the importance of molecular profiling will be shown in a representative series of CNS neoplasms including both the most frequent tumor types and other selected entities for which molecular characterization plays a critical role.

LP-57: Increasing Confidence in New Approach Methodologies for Inhalation Risk Assessment with Multiple End Point Assays Using 5-day RepeatExposure to 1,3-dichloropropene

LP-57: Increasing Confidence in New Approach Methodologies for Inhalation Risk Assessment with Multiple End Point Assays Using 5-day RepeatExposure to 1,3-dichloropropene

Retrospective immunophenotypical evaluation of MET, PD-1/PD-L1, and mTOR pathways in primary tumors and pulmonary metastases of renal cell carcinoma: the RIVELATOR study addresses the issue of biomarkers heterogeneity.

In renal cell carcinoma (RCC), tumor heterogeneity generated challenges to biomarker development and therapeutic management, often becoming responsible for primary and acquired drug resistance. This study aimed to assess the inter-tumoral, intra-tumoral, and intra-lesional heterogeneity of known druggable targets in metastatic RCC (mRCC). The RIVELATOR study was a monocenter retrospective analysis of biological samples from 25 cases of primary RCC and their paired pulmonary metastases. The biomarkers analyzed included MET, mTOR, PD-1/PD-L1 pathways and the immune context. High multi-level heterogeneity was demonstrated. MET was the most reliable biomarker, with the lowest intratumor heterogeneity: the positive mutual correlation between MET expression in primary tumors and their metastases had a significantly proportional intensity (P = 0.038). The intratumor heterogeneity grade was significantly higher for the mTOR pathway proteins. Combined immunophenotypical expression patterns and their correlations with the immune context were uncovered [i.e., mTOR expression in the metastases positively correlated with PD-L1 expression in tumor-infiltrating lymphocytes (TILs), P = 0.019; MET expression was related to PD-1 expression on TILs (P = 0.041, ρ = 0.41) and peritumoral lymphocytes (RILs; P = 0.013, ρ = 0.49)], suggesting the possibility of predicting drug response or resistance to tyrosine kinase, mTOR, or immune checkpoint inhibitors. In mRCC, multiple and multi-level assays of potentially predictive biomarkers are needed for their reliable translation into clinical practice. The easy-to-use immunohistochemical method of the present study allowed the identification of different combined expression patterns, providing cues for planning the management of systemic treatment combinations and sequences in an mRCC patient population. The quantitative heterogeneity of the investigated biomarkers suggests that multiple intralesional assays are needed to consider the assessment reliable for clinical considerations.

Determining the Efficacy of Polyphenols in Inhibiting the Aggregation of Amyloid Beta Proteins

Alzheimer's Disease is caused by an aggregation of amyloid beta and tau proteins in the brain. Polyphenols, a broad class of naturally-existing compounds, have been shown to inhibit the aggregation of those proteins. This project aims to focus on expressing different combinations of those proteins, as well as assaying those proteins for aggregation inhibition using polyphenols such as curcumin, caffeic acid, epigallocatechin gallate (EGCG), and more to determine which polyphenol is most effective in doing so. We chose to use these polyphenols because of their past precedence in other work, along with their widespread prevalence. However, this project focused more on the biological and in-vitro aspect of polyphenols inhibiting amyloid beta, such as conducting multiple assays including Congo Red, Avoidance, and Dynamic Light Scattering in order to receive tangible results. Through our studies, we found that polyphenols do produce an inhibitory effect on the aggregation of amyloid-beta.

Iron and Copper Alter the Oxidative Potential of Secondary Organic Aerosol: Insights from Online Measurements and Model Development.

The oxidative potential (OP) of particulate matter has been widely suggested as a key metric for describing atmospheric particle toxicity. Secondary organic aerosol (SOA) and redox-active transition metals, such as iron and copper, are key drivers of particle OP. However, their relative contributions to OP, as well as the influence of metal-organic interactions and particulate chemistry on OP, remains uncertain. In this work, we simultaneously deploy two novel online instruments for the first time, providing robust quantification of particle OP. We utilize online AA (OPAA) and 2,7-dichlorofluoroscein (ROSDCFH) methods to investigate the influence of Fe(II) and Cu(II) on the OP of secondary organic aerosol (SOA). In addition, we quantify the OH production (OPOH) from these particle mixtures. We observe a range of synergistic and antagonistic interactions when Fe(II) and Cu(II) are mixed with representative biogenic (β-pinene) and anthropogenic (naphthalene) SOA. A newly developed kinetic model revealed key reactions among SOA components, transition metals, and ascorbate, influencing OPAA. Model predictions agree well with OPAA measurements, highlighting metal-ascorbate and -naphthoquinone-ascorbate reactions as important drivers of OPAA. The simultaneous application of multiple OP assays and a kinetic model provides new insights into the influence of metal and SOA interactions on particle OP.

Comparison of SARS-CoV-2 RT-PCR Ct Values across Multiple Assays with Different Targets.

Comparison of SARS-CoV-2 RT-PCR Ct Values across Multiple Assays with Different Targets.

Quantitative and Multiplexed Chopper-Based Time-Gated Imaging for Bioanalysis on a Smartphone.

Smartphones are emerging platforms for point-of-care diagnostics (POCDs), where the on-board camera is, for example, used to image fluorescence. Many laboratory instruments are capable of time-gated (TG) photoluminescence (PL) measurements─an analytical method leveraged by multiple commercial assay kits. When paired with long-lived PL emitters such as luminescent lanthanide complexes (LLCs), time-gating eliminates background from sample autofluorescence and many other sources. This capability is amenable to minimally processed samples and would thus be useful for POCDs on a smartphone-based platform. Here, we report a double-chopper design for TG PL imaging using a portable, 3D-printed, smartphone-based device. The rotation speed, dimensions, and overlap of the chopper blades and gaps set the timing parameters, with delay times on the order of hundreds of microseconds to milliseconds. The device was capable of quantitative TG imaging of PL from terbium(III) and europium(III) LLCs, including rejection of short-lived PL background from serum and tissue phantoms, spectral and temporal multiplexing, a model time-gated Förster resonance energy transfer (TG-FRET) assay, and imaging of cells. As the first smartphone-based demonstrations of these important analytical capabilities, this work is an important foundation for developing POCD methods based on TG PL imaging.

DNA methylation-based testing in peripheral blood mononuclear cells enables accurate and early detection of colorectal cancer.

An effective blood-based method for the diagnosis of colorectal cancer (CRC) has not yet been developed. Molecular alterations of immune cells occur early in tumorigenesis, providing the theoretical underpinning for early cancer diagnosis based on immune cell profiling. Therefore, we aimed to develop an effective detection method based on peripheral blood mononuclear cells (PBMCs) to improve the diagnosis of CRC. Analysis of the genome-wide methylation landscape of PBMCs from CRC patients and healthy controls by microarray, pyrosequencing, and targeted bisulfite sequencing revealed five DNA methylation markers for CRC diagnosis, especially early-stage CRC (eCRC). A single-tube multiple methylation-specific quantitative PCR assay (multi-msqPCR) for simultaneous detection of five methylation markers was established, which allowed quantitative analysis of samples with as little as 0.1% PBMC DNA and had better discriminative performance than single-molecule detection. Then, a CRC diagnostic model (CDM) based on methylation markers and the multi-msqPCR method was constructed that achieved high accuracy for eCRC (AUC=0.91; sensitivity=81.18%; specificity=89.39%), which was improved compared to CEA (AUC=0.79). The CDM also enabled a high degree of discrimination for advanced adenoma (AA) cases (AUC=0.85, sensitivity=63.04%). Follow-up data also demonstrated that the CDM could identify CRC potential up to 2 years before currently used diagnostic methods. In conclusion, the approach constructed in this study based on PBMC-derived DNA methylation markers and a multi-msqPCR method is a promising and easily implementable diagnostic method for eCRC.