Reporter Gene Assays

Genetically engineered secretory horseradish peroxidase is a sensitive, stable, and affordable non-lytic reporter gene system for real-time promoter activity management

A light-producing secretory protein that is collectible through the supernatant of a culture medium is essential in a cell-based reporter gene system and allows for real-time monitoring of upstream events of a promoter. Compared to other secretory luciferases, Cypridina luciferase (CLuc) coupled with vargulin emits the brightest signal; however, the signal half-life suffers constantly from the fast oxidation process of the substrate, resulting in a rapid signal depletion, which makes the detection signal short and unstable. In this study, we aimed to develop a new reporter gene system with a more stable signal and lower cost, whilst retaining sensitivity comparable to the CLuc reporter gene system. To this end, we genetically engineered horseradish peroxidase (HRP) to be secreted with mammalian cells. The secreted form HRP (sHRP) was then used as a proof-of-concept of real-time cell signaling management. First, we made sure that HRP retained its enzymatic function with our genetic engineering process and confirmed that it was collectable and suitable for side-by-side comparison with CLuc. sHRP showed comparable sensitivity, 7 to 80 times more signal half-life compared to CLuc, and precisely reported NF-κB-regulated promoter in response to stimulation with TNF-α. sHRP was not affected by multiple cell culturing media and was calculated to be at least 9 times cheaper than the CLuc reporter gene system. Thus, sHRP offers new insight into the reporter gene system for drug screening and intracellular signaling management and provides a precise, sustainable and affordable operating environment.

The latest progress in assay development in leishmaniasis drug discovery: a review of the available papers on PubMed from the past year

INTRODUCTION

Leishmaniasis is a significant neglected tropical disease with limited treatment options that urgently requires ongoing efforts in drug discovery. Recent advances have focused on the development of new assays and methods to identify effective therapeutic candidates.

AREAS COVERED

This review explores recent trends and methodologies in leishmaniasis drug discovery, with a particular focus on in silico and in vitro studies, as well as in vivo validation, using animal models. A detailed analysis of recent studies was provided, discussing the methodologies employed, such as manual and automated parasite quantification, and the use of fluorescence and luminescence-based techniques. Additionally, global research trends were analyzed, highlighting the leading countries in scientific output and the collaborative efforts driving advancements in this field.

EXPERT OPINION

The field of leishmaniasis drug discovery has rapidly progressed in the last years, but the lack of standardized methodologies and limited in vivo validation remain significant hurdles. To advance promising treatments to clinical trials, cross-validation of preclinical findings and interdisciplinary collaboration are essential. Increased funding and global partnerships are also crucial to accelerate the discovery and development of alternative and effective therapies.

Design considerations when creating a high throughput screen-compatible in vitro model of osteogenesis

Inducing osteogenic differentiation in vitro is useful for the identification and development of bone regeneration therapies as well as modelling bone disorders. To couple in vitro models with high throughput screening techniques retains the assay's relevance in research while increasing its therapeutic impact. Miniaturizing, automating and/or digitalizing in vitro assays will reduce the required quantity of cells, biologic stimulants, culture/output assay reagents, time and cost. This review highlights the design and workflow considerations for creating a high throughput screen-compatible model of osteogenesis, comparing and contrasting osteogenic cell type, assay fabrication and culture methodology, osteogenic induction approach and repurposing existing output techniques.

Development and application of potency assays based on genetically modified cells for biological products

Potency assays are key to the development, registration, and quality control of biological products. Although previously preferred for clinical relevance, in vivo bioassays have greatly diminished with the advent of dependent cell lines as well as due to ethical concerns. However, for some products, the development of in vitro cell-based assay is challenging, or existing method has limitations such as tedious procedure or low sensitivity. The generation of genetically modified (GM) cell line with improved response to the analyte provides a scientific and promising solution. Potency assays based on GM cell lines are currently used for the quality control of biological products including cytokines, hormones, therapeutic antibodies, vaccines and gene therapy products. In this review, we have discussed the general principles of designing and developing GM cells-based potency assays, including identification of cellular signaling pathways and detectable biological effects, generation of responsive cell lines and constitution of test systems, based on the current research progress. In addition, the applications of some novel technologies and the common concerns regarding GM cells have also been discussed. The research presented in this review provides insights for the development and application of novel GM cells-based potency assays for biological products.

PlotXpress, a webtool for normalization and visualization of reporter expression data

In molecular cell biology, reporter assays are frequently used to investigate gene expression levels. Reporter assays employ a gene that encodes a light-emitting protein, of which the luminescence is quantified as a proxy of gene expression. Commercial parties provide reporter assay kits that include protocols and specialized detection machinery. However, downstream analysis of the output data and their presentation are not standardized. We have developed plotXpress to fill this gap, providing a free, open-source platform for the semi-automated analysis and standardized visualisation of experimental gene reporter data. Users can upload raw luminescence data acquired from a reporter gene assay with an internal control. In plotXpress, the data is corrected for sample variation with the internal control and the average for each condition is calculated. When a reference condition is selected the fold change is calculated for all other conditions, based on the selected reference. The results are shown as dot plots with a statistical summary, which can be adjusted to create publication-grade plots without requiring coding skills. Altogether, plotXpress is an open-source, low-threshold, web-based tool, that promotes a standardized and reproducible analysis while providing an appealing visualization of reporter data. The webtool can be accessed at: https://huygens.science.uva.nl/PlotXpress/

High-Throughput Screening: today's biochemical and cell-based approaches

High-throughput screening (HTS) provides starting chemical matter in the adventure of developing a new drug. In this review, we survey several HTS methods used today for hit identification, organized in two main flavors: biochemical and cell-based assays. Biochemical assays discussed include fluorescence polarization and anisotropy, FRET, TR-FRET, and fluorescence lifetime analysis. Binding-based methods are also surveyed, including NMR, SPR, mass spectrometry, and DSF. On the other hand, cell-based assays discussed include viability, reporter gene, second messenger, and high-throughput microscopy assays. We devote some emphasis to high-content screening, which is becoming very popular. An advisable stage after hit discovery using phenotypic screens is target deconvolution, and we provide an overview of current chemical proteomics, in silico, and chemical genetics tools. Emphasis is made on recent CRISPR/dCas-based screens. Lastly, we illustrate some of the considerations that inform the choice of HTS methods and point to some areas with potential interest for future research.

Approaching complexity: systems biology and ms-based techniques to address immune signaling

INTRODUCTION

Studying immune signaling has been critical for our understanding of immunology, pathogenesis, cancer, and homeostasis. To enhance the breadth of the analysis, high throughput methods have been developed to survey multiple areas simultaneously, including transcriptomics, reporter assays, and ELISAs. While these techniques have been extremely informative, mass-spectrometry-based technologies have been gaining momentum and starting to be widely used in the studies of immune signaling and systems immunology.

AREAS COVERED

We present established proteomic methods that have been used to address immune signaling and discuss the new mass-spectrometry- based techniques of interest to the expanding field of systems immunology. Established and new proteomic methods and their applications discussed here include post-translational modification analysis, protein quantification, secretome analysis, and interactomics. In addition, we present developments in small molecule and metabolite analysis, mass spectrometry imaging, and single cell analysis. Finally, we discuss the role of multi-omic integration in aiding leading edge investigation.

EXPERT OPINION

In science, available techniques enhance the breadth and depth of the studies. By incorporating proteomic techniques and their innovative use, it will be possible to expand the current studies and to address novel questions at the forefront of scientific discovery.

The Identification and Interpretation of cis-Regulatory Noncoding Mutations in Cancer

In the need to characterise the genomic landscape of cancers and to establish novel biomarkers and therapeutic targets, studies have largely focused on the identification of driver mutations within the protein-coding gene regions, where the most pathogenic alterations are known to occur. However, the noncoding genome is significantly larger than its protein-coding counterpart, and evidence reveals that regulatory sequences also harbour functional mutations that significantly affect the regulation of genes and pathways implicated in cancer. Due to the sheer number of noncoding mutations (NCMs) and the limited knowledge of regulatory element functionality in cancer genomes, differentiating pathogenic mutations from background passenger noise is particularly challenging technically and computationally. Here we review various up-to-date high-throughput sequencing data/studies and in silico methods that can be employed to interrogate the noncoding genome. We aim to provide an overview of available data resources as well as computational and molecular techniques that can help and guide the search for functional NCMs in cancer genomes.

Firefly Luciferase Mutant with Enhanced Activity and Thermostability

The luciferase isolated from the firefly Photinus pyralis (Ppy) catalyzes a two-step reaction that results in the oxidation of d-luciferin accompanied by emission of yellow-green light with a peak at 560 nm. Among many applications, Ppy luciferase has been used extensively as a reporter gene in living cells and organisms. However, some biological applications are limited by the low stability of the luciferase and limited intracellular luciferin concentration. To address these challenges, efforts to protein engineer Ppy luciferase have resulted in a number of mutants with improved properties such as thermostability, pH tolerance, and catalytic turn over. In this work, we combined amino acid mutations that were shown to enhance the enzyme's thermostability (Mutant E) with those reported to enhance catalytic activity (LGR). The resulting mutant (YY5) contained eight amino acid changes from the wild-type luciferase and exhibited both improved thermostability and brighter luminescence at low luciferin concentrations. Therefore, YY5 may be useful for reporter gene applications.

A multiplexed screening method for pluripotency

Measurement of Alkaline Phosphatase (ALP) level is a widely used procedure in clinical and basic research. We present a simple and inexpensive luminescence-based method that allows multiplexed measurement and normalization of intracellular ALP levels in one sample well. The method comprises two commercially available reagents enabling quantification of ALP levels and cell number by two sequential luminescence readouts. Using this method we were able to detect and analyze somatic reprogramming into pluripotent stem cells. The method is highly applicable for High Throughput Screening (HTS) campaigns and analysis.

Exogenous gene integration mediated by genome editing technologies in zebrafish

Genome editing technologies, such as transcription activator-like effector nuclease (TALEN) and the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems, can induce DNA double-strand breaks (DSBs) at the targeted genomic locus, leading to frameshift-mediated gene disruption in the process of DSB repair. Recently, the technology-induced DSBs followed by DSB repairs are applied to integrate exogenous genes into the targeted genomic locus in various model organisms. In addition to a conventional knock-in technology mediated by homology-directed repair (HDR), novel knock-in technologies using refined donor vectors have also been developed with the genome editing technologies based on other DSB repair mechanisms, including non-homologous end joining (NHEJ) and microhomology-mediated end joining (MMEJ). Therefore, the improved knock-in technologies would contribute to freely modify the genome of model organisms.

A red fluorescent protein (DsRED) from Discosoma sp. as a reporter for gene expression in walnut somatic embryos

KEY MESSAGE

An improved scorable marker was developed for somatic embryo transformation. This method is more reliable than GFP and provides more efficient embryo selection than β-glucuronidase assays (GUS, MUG). Reporter genes are widely used to select transformed cells and tissues. Fluorescent proteins have become an integral part of live-cell imaging research over the past 10 years. DsRED is an ideal reporter for avoiding plant chlorophyll autofluorescence and for double labeling in combination with other scorable markers. In this study, we transformed walnut somatic embryos with a construct containing the DsRED-expressing binary vector pKGW-RR to assess the effect of this red fluorescent protein visual reporter on both embryos and regenerated plants. Results showed that DsRED expression was apparent with maximum brightness at 7-10 days after initiation. Fourteen of twenty-four surviving somatic embryos were bright red. These E0 embryos generated 25 wholly fluorescent E1 embryos and 43 wholly fluorescent E2 embryos at 2 weeks intervals. The germination percentage of DsRED-positive embryos was greater than 80% and gave rise to 45 fluorescent transgenic walnut plants. The regenerated transgenic plants expressed DsRED in all tissues examined including transverse sections of vegetative organs. The percentage of transformed plants that developed roots (48.3%) was similar to control shoots (53%). For transformation of walnut somatic embryos, the DsRED-based reporter system is more stable and reliable than green fluorescent protein (GFP) and, since it is a directly read and non-destructive assay, it provides a more efficient means of monitoring transformation than β-glucuronidase (GUS).