High-throughput Screening Analysis Research Articles

Fluorescent riboswitch-controlled biosensors for the genome scale analysis of metabolic pathways

Fluorescent detection in cells has been tremendously developed over the years and now benefits from a large array of reporters that can provide sensitive and specific detection in real time. However, the intracellular monitoring of metabolite levels still poses great challenges due to the often complex nature of detected metabolites. Here, we provide a systematic analysis of thiamin pyrophosphate (TPP) metabolism in Escherichia coli by using a TPP-sensing riboswitch that controls the expression of the fluorescent gfp reporter. By comparing different combinations of reporter fusions and TPP-sensing riboswitches, we determine key elements that are associated with strong TPP-dependent sensing. Furthermore, by using the Keio collection as a proxy for growth conditions differing in TPP levels, we perform a high-throughput screen analysis using high-density solid agar plates. Our study reveals several genes whose deletion leads to increased or decreased TPP levels. The approach developed here could be applicable to other riboswitches and reporter genes, thus representing a framework onto which further development could lead to highly sophisticated detection platforms allowing metabolic screens and identification of orphan riboswitches.

The determination of mycotoxins using isotope-coded labeling and dispersive liquid–liquid microextraction by high throughput flow injection analysis coupled with tandem mass spectrometry

A novel and rapid method for the determination of ochratoxin A (OTA), funmonisin B1 (FB1) and zearalenone (ZEN) in legumes samples by high throughput flow injection analysis-tandem mass spectrometry (FIA-MS/MS) in conjunction with isotope-coded labeling (ICD) coupled with dispersive liquid–liquid microextraction (DLLME) was developed. The samples were extracted by a known QuEChERS method (Quick, Easy, Cheap, Effective, Rugged, Safe). The extracted components and mycotoxin standards were, respectively, labeled by d0-10-methyl-acridone-2-sulfonyl chloride and its deuterated counter part (d3-MASC). Subsequently, the mixed light-/heavy-labeled solutions were enriched and purified by DLLME method and corresponding extracts were directly used for FIA-MS/MS analysis. The FIA-MS/MS method coupled with ICD-coded labeling technique for the determination of mycotoxins in legume samples could be achieved within 2 min, which was much suitable for high throughput screening analysis. Meanwhile, the labeled mycotoxins with d3-MASC as internal standards could effectively eliminate matrix interference and ensure the accuracy and precision of mass spectrometry analysis. The limits of detection (LODs) and the limits of quantification (LOQs) ranged from 0.29 to 0.42 μg/L and 0.85 to 1.30 μg/L, respectively. The recoveries were 66.9 %–85.2 %, and the daily and inter day RSDs were within the range of 2.0 %–4.9 % and 2.4 %–5.0 %, respectively. The established method could be feasibility applied to the determination of mycotoxins in legume samples with satisfactory results.

Post-modified linker functionalization of metal organic frameworks for high-efficiency adsorption and quantification of trace organophosphorus pesticides in environmental water

Water pollution caused by organophosphorus pesticides (OPPs) from agricultural production causes vital great threat to mankind lives and thus developing a method for rapid removal and detection of OPPs is urgent. In this work, we proposed the linker functionalization of metal organic frameworks (UiO-66) by post-modification to generate defects and active sites for tailoring their adsorption behavior. The metal organic frameworks (MOFs) modified by functional groups (amino and pyridine) exhibited similar physicochemical property and pore structure. The UiO-66-PA exhibited an excellent performance of rapid adsorption of OPPs in water with average capacity of 246.55 mg/g. Experimental characterizations and theoretical simulations revealed that the enhanced binding energy between UiO-66-PA and OPPs resulted from synergistic interaction between pyridine and OPPs via nucleophilic effect, π-π interaction, and metal electronic interaction, boosting the adsorption capacity and removal efficiency, which suggested that functional group plays important role in improving performance. When used it as adsorbent for analysis of OPPs in water coupled with ambient ionization source, UiO-66-PA exhibited an excellent performance of the quantitative detection of OPPs in water with limit of detections (LODs) of 0.076–––0.251 ng/mL and relative standard deviations (RSDs) of 1.13 % − 5.84 %. In addition, the proposed analytical method could be applied in analysis of three environmental water samples with great sensitivity, anti-interference and reusability, which demonstrated that UiO-66-PA afforded outstanding selectivity for OPPs and could be appropriate for high-throughput screening and on-site analysis. This work could provide a novel method to design MOFs-based adsorbents with functions of removal and purification via post-modification and exhibit a great potential to rapid analysis of OPPs in environmental water.

Build Borophite from Borophenes: A Boron Analogue Graphite.

Unlike graphene derived from graphite, borophenes represent a distinct class of synthetic two-dimensional materials devoid of analogous bulk-layered allotropes, leading to covalent bonding within borophenes instead of van der Waals (vdW) stacking. Our investigation focuses on 665 vdW-stacking boron bilayers to uncover potential bulk-layered boron allotropes through vdW stacking. Systematic high-throughput screening and stability analysis reveal a prevailing inclination toward covalently bonded layers in the majority of boron bilayers. However, an intriguing outlier emerges in δ5 borophene, demonstrating potential as a vdW-stacking candidate. We delve into electronic and topological structural similarities between δ5 borophene and graphene, shedding light on the structural integrity and stability of vdW-stacked boron structures across bilayers, multilayers, and bulk-layered allotropes. The δ5 borophene analogues exhibit metallic properties and characteristics of phonon-mediated superconductors, boasting a critical temperature near 22 K. This study paves the way for the concept of "borophite", a long-awaited boron analogue of graphite.

Integrating microfluidics and synthetic biology: advancements and diverse applications across organisms.

Synthetic biology is the design and modification of biological systems for specific functions, integrating several disciplines like engineering, genetics, and computer science. The field of synthetic biology is to understand biological processes within host organisms through the manipulation and regulation of their genetic pathways and the addition of biocontrol circuits to enhance their production capabilities. This pursuit serves to address global challenges spanning diverse domains that are difficult to tackle through conventional routes of production. Despite its impact, achieving precise, dynamic, and high-throughput manipulation of biological processes is still challenging. Microfluidics offers a solution to those challenges, enabling controlled fluid handling at the microscale, offering lower reagent consumption, faster analysis of biochemical reactions, automation, and high throughput screening. In this review, we diverge from conventional focus on automating the synthetic biology design-build-test-learn cycle, and instead, focus on microfluidic platforms and their role in advancing synthetic biology through its integration with host organisms - bacterial cells, yeast, fungi, animal cells - and cell-free systems. The review illustrates how microfluidic devices have been instrumental in understanding biological systems by showcasing microfluidics as an essential tool to create synthetic genetic circuits, pathways, and organisms within controlled environments. In conclusion, we show how microfluidics expedite synthetic biology applications across diverse domains including but not limited to personalized medicine, bioenergy, and agriculture.

Discovery of PLD4 modulators by high-throughput screening and kinetic analysis

Phospholipase D3 (PLD3) and D4 (PLD4) are endolysosomal exonucleases of ssDNA and ssRNA that regulate innate immunity. Polymorphisms of these enzymes are correlated with numerous human diseases, including Alzheimer’s, rheumatoid arthritis, and systemic sclerosis. Pharmacological modulation of these immunoregulatory proteins may yield novel immunotherapies and adjuvants. A previous study reported a high-throughput screen (N = 17,952) that discovered a PLD3-selective activator and inhibitor, as well as a nonselective inhibitor, but failed to identify selective modulators of PLD4. However, modulators selective for PLD4 are therapeutically pertinent, since recent reports have shown that regulating this protein has direct implications in cancer and autoimmune diseases. Furthermore, the high expression of PLD4 in dendritic and myeloid cells, in comparison to the broader expression of PLD3, presents the opportunity for a cell-targeted immunotherapy. Here, we describe the screening of an expanded diversity library (N = 45,760) with an improved platform and report the discovery of one inhibitor and three activators selective for PLD4. Furthermore, kinetic modeling and structural analysis suggest mechanistic differences in the modulation of these hits. These findings further establish the utility of this screening platform and provide a set of chemical scaffolds to guide future small-molecule development for this novel immunoregulator target.

Drug Responses in Plexiform Neurofibroma Type I (PNF1) Cell Lines Using High-Throughput Data and Combined Effectiveness and Potency.

Background: Neurofibromatosis type 1 (NF1) is a genetic disorder characterized by heterozygous germline NF1 gene mutations that predispose patients to developing plexiform neurofibromas, which are benign but often disfiguring tumors of the peripheral nerve sheath induced by loss of heterozygosity at the NF1 locus. These can progress to malignant peripheral nerve sheath tumors (MPNSTs). There are no approved drug treatments for adults with NF1-related inoperable plexiform neurofibromas, and only one drug (selumetinib), which is an FDA-approved targeted therapy for the treatment of symptomatic pediatric plexiform neurofibromas, highlighting the need for additional drug screening and development. In high-throughput screening, the effectiveness of drugs against cell lines is often assessed by measuring in vitro potency (AC50) or the area under the curve (AUC). However, the variability of dose-response curves across drugs and cell lines and the frequency of partial effectiveness suggest that these measures alone fail to provide a full picture of overall efficacy. Methods: Using concentration-response data, we combined response effectiveness (EFF) and potency (AC50) into (a) a score characterizing the effect of a compound on a single cell line, S = log[EFF/AC50], and (b) a relative score, ΔS, characterizing the relative difference between a reference (e.g., non-tumor) and test (tumor) cell line. ΔS was applied to data from high-throughput screening (HTS) of a drug panel tested on NF1-/- tumor cells, using immortalized non-tumor NF1+/- cells as a reference. Results: We identified drugs with sensitivity, targeting expected pathways, such as MAPK-ERK and PI3K-AKT, as well as serotonin-related targets, among others. The ΔS technique used here, in tandem with a supplemental ΔS web tool, simplifies HTS analysis and may provide a springboard for further investigations into drug response in NF1-related cancers. The tool may also prove useful for drug development in a variety of other cancers.

High-throughput droplet microfluidics screening and genome sequencing analysis for improved amylase-producing Aspergillus oryzae

BackgroundThe exceptional protein secretion capacity, intricate post-translational modification processes, and inherent safety features of A. oryzae make it a promising expression system. However, heterologous protein expression levels of existing A. oryzae species cannot meet the requirement for industrial-scale production. Therefore, establishing an efficient screening technology is significant for the development of the A. oryzae expression system.ResultsIn this work, a high-throughput screening method suitable for A. oryzae has been established by combining the microfluidic system and flow cytometry. Its screening efficiency can reach 350 droplets per minute. The diameter of the microdroplet was enlarged to 290 µm to adapt to the polar growth of A. oryzae hyphae. Through enrichment and screening from approximately 450,000 droplets within 2 weeks, a high-producing strain with α-amylase increased by 6.6 times was successfully obtained. Furthermore, 29 mutated genes were identified by genome resequencing of high-yield strains, with 15 genes subjected to editing and validation. Two genes may individually influence α-amylase expression in A. oryzae by affecting membrane-associated multicellular processes and regulating the transcription of related genes.ConclusionsThe developed high-throughput screening strategy provides a reference for other filamentous fungi and Streptomyces. Besides, the strains with different excellent characteristics obtained by efficient screening can also provide materials for the analysis of genetic and regulatory mechanisms in the A. oryzae expression system.

Using the structural diversity of RNA: protein interfaces to selectively target RNA with small molecules in cells: methods and perspectives.

In recent years, RNA has gained traction both as a therapeutic molecule and as a therapeutic target in several human pathologies. In this review, we consider the approach of targeting RNA using small molecules for both research and therapeutic purposes. Given the primary challenge presented by the low structural diversity of RNA, we discuss the potential for targeting RNA: protein interactions to enhance the structural and sequence specificity of drug candidates. We review available tools and inherent challenges in this approach, ranging from adapted bioinformatics tools to in vitro and cellular high-throughput screening and functional analysis. We further consider two critical steps in targeting RNA/protein interactions: first, the integration of in silico and structural analyses to improve the efficacy of molecules by identifying scaffolds with high affinity, and second, increasing the likelihood of identifying on-target compounds in cells through a combination of high-throughput approaches and functional assays. We anticipate that the development of a new class of molecules targeting RNA: protein interactions to prevent physio-pathological mechanisms could significantly expand the arsenal of effective therapeutic compounds.

High-throughput screening of ancient forest plant extracts shows cytotoxicity towards triple-negative breast cancer

According to the World Health Organization, women's breast cancer is among the most common cancers with 7.8 million diagnosed cases during 2016–2020 and encompasses 15 % of all female cancer-related mortalities. These mortality events from triple-negative breast cancer are a significant health issue worldwide calling for a continuous search of bioactive compounds for better cancer treatments. Historically, plants are important sources for identifying such new bioactive chemicals for treatments. Here we use high-throughput screening and mass spectrometry analyses of extracts from 100 plant species collected in Chinese ancient forests to detect novel bioactive breast cancer phytochemicals. First, to study the effects on viability of the plant extracts, we used a MTT and CCK-8 cytotoxicity assay employing triple-negative breast cancer (TNBC) MDA-MB-231 and normal epithelial MCF-10A cell lines and cell cycle arrest to estimate apoptosis using flow cytometry for the most potent three speices. Based on these analyses, the final most potent extracts were from the Amur honeysuckle (Lonicera maackii) wood/root bark and Nigaki (Picrasma quassioides) wood/root bark. Then, 5 × 106 MDA-MB-231 cells were injected subcutaneously into the right hind leg of nude mice and a tumour was allowed to grow before treatment for seven days. Subsequently, the four exposed groups received gavage extracts from Amur honeysuckle and Nigaki (Amur honeysuckle wood distilled water, Amur honeysuckle root bark ethanol, Nigaki wood ethanol or Nigaki root bark distilled water/ethanol (1:1) extracts) in phosphate-buffered saline (PBS), while the control group received only PBS. The tumour weight of treated nude mice was reduced significantly by 60.5 % within 2 weeks, while on average killing 70 % of the MDA-MB-231 breast cancer cells after 48 h treatment (MTT test). In addition, screening of target genes using the Swiss Target Prediction, STITCH, STRING and NCBI-gene database showed that the four plant extracts possess desirable activity towards several known breast cancer genes. This reflects that the extracts may kill MBD-MB-231 breast cancer cells. This is the first screening of plant extracts with high efficiency in 2 decades, showing promising results for future development of novel cancer treatments.

High-throughput screening and quantitative analysis of hidden ingredients in plant protection products by GC-MS/MS

Hidden ingredients in plant protection products (PPPs) threaten public health, food trade, and the environment. In this study, we developed a high-throughput screening method of 639 hidden ingredients in PPPs using GC-MS/MS in multiple reaction monitoring mode. Results showed that the qualitative criteria of retention time (tR) shift and uncertainty of qualifier to quantifier ratio in the commercially available Shimadzu Smart Pesticides Database were set at < 0.17 min and < 30%, respectively, which could be used to tentatively identify compounds without standards. The limits of quantification were 0.01–0.05 mg/kg. A wide linear range of 10–1000 μg/L was observed with R2 ≥ 0.975. Recoveries from three types of PPP formulations were 62.08%− 126.3%, with relative standard deviations < 15.7%. Finally, this method was applied to screen and quantify hidden ingredients in 91 plant protection products (PPPs) samples collected from online sales in China. Only one hidden ingredient, dimethomorph (1.6 g/kg), was detected in the polyoxin formulation (15% wettable powder). The results will be helpful in assessing the potential risks of hidden ingredients in PPPs.

Integrated High-Throughput Screening and Large-Scale Isobolographic Analysis to Accelerate the Discovery of Radiosensitizers With Greater Selectivity for Cancer Cells

High-throughput screening (HTS) platforms have been widely used to identify candidate anticancer drugs and drug-drug combinations; however, HTS-based identification of new drug-ionizing radiation (IR) combinations has rarely been reported. Herein, we developed an integrated approach including cell-based HTS and computational large-scale isobolographic analysis to accelerate the identification of radiosensitizing compounds acting strongly and more specifically on cancer cells. In a 384-well plate format, 160 compounds likely to interfere with the cell response to radiation were screened on human glioblastoma (U251-MG) and cervix carcinoma (ME-180) cell lines, as well as on normal fibroblasts (CCD-19Lu). After drug exposure, cells were irradiated or not and short-term cell survival was assessed by high-throughput cell microscopy. Computational large-scale dose-response and isobolographic approach were used to identify promising synergistic drugs radiosensitizing cancer cells rather than normal cells. Synergy of a promising compound was confirmed on ME-180 cells by an independent 96-well assay protocol, and finally, by the gold-standard colony forming assay. We retained 4 compounds synergistic at 2 isoeffects in U251-MG and ME-180 cell lines and 11 compounds synergistically effective in only one cancer cell line. Among these 15 promising radiosensitizers, 5 compounds showed limited toxicity combined or not with IR on normal fibroblasts. Overall, this study demonstrated that HTS chemoradiation screening together with large-scale computational analysis is an efficient tool to identify synergistic drug-IR combinations, with concomitant assessment of unwanted toxicity on normal fibroblasts. It sparks expectations to accelerate the discovery of highly desired agents improving the therapeutic index of radiation therapy.

Recognition, possible source, and risk assessment of organic pollutants in surface water from the Yongding River Basin by non-target and target screening

Organic pollutants in aquatic environment could have important implications on pollution stress on aquatic organisms and even on the risk of human exposure. Thus, revealing their occurrence in aquatic environment is essential for water quality monitoring and ecological risk purposes. In this study, a comprehensive two-dimensional gas chromatography connected with time-of-flight mass spectrometry (GC × GC-TOF-MS) was applied, to enable non-target and target analysis of pollutants in the Yongding River Basin. Based on the isotopic patterns, accurate masses and standard substances, certain environmental contaminants were tentatively identified which including polycyclic aromatic hydrocarbon (PAHs), organochlorine pesticides (OCPs), phenols, amines, etc. The compounds with the highest concentration were naphthalene (109.0 ng/L), 2,3-benzofuran (51.5 ng/L) and 1,4-dichlorobenzene (35.9 ng/L) in Guishui River. Wastewater treatment plants (WWTPs) discharges were a main source of pollutants in Yongding River Basin, as the types of compounds screened in the downstream river were relatively similar to those from WWTPs. According to the target analysis, a number of pollutants were selected due to the acute toxicity and cumulative discharge from WWTPs and downstream rivers. Three PAHs (naphthalene, Benzo(b)fluoranthene and pyrene) homologues showed moderate risk to fish and H. Azteca in Yongding River Basin, while the rest of the measured chemicals showed low ecological impact across the entire study area based on the risk assessment. The results are helpful for understanding the necessity of high-throughput screening analysis for assessing water quality of rivers and the discharge emissions of pollutants from WWTPs to the river environment.

Simplicity: Web-Based Visualization and Analysis of High-Throughput Cancer Cell Line Screens.

High-throughput drug screens are a powerful tool for cancer drug development. However, the results of such screens are often made available only as raw data, which is intractable for researchers without informatics skills, or as highly processed summary statistics, which can lack essential information for translating screening results into clinically meaningful discoveries. To improve the usability of these datasets, we developed Simplicity, a robust and user-friendly web interface for visualizing, exploring, and summarizing raw and processed data from high- throughput drug screens. Importantly, Simplicity allows for easy recalculation of summary statistics at user-defined drug concentrations. This allows Simplicity's outputs to be used with methods that rely on statistics being calculated at clinically relevant doses. Simplicity can be freely accessed at https://oncotherapyinformatics.org/simplicity/.

Bioprinted Hydrogels for Fibrosis and Wound Healing: Treatment and Modeling.

Three-dimensional (3D) printing has been used to fabricate biomaterial scaffolds with finely controlled physical architecture and user-defined patterning of biological ligands. Excitingly, recent advances in bioprinting have enabled the development of highly biomimetic hydrogels for the treatment of fibrosis and the promotion of wound healing. Bioprinted hydrogels offer more accurate spatial recapitulation of the biochemical and biophysical cues that inhibit fibrosis and promote tissue regeneration, augmenting the therapeutic potential of hydrogel-based therapies. Accordingly, bioprinted hydrogels have been used for the treatment of fibrosis in a diverse array of tissues and organs, including the skin, heart, and endometrium. Furthermore, bioprinted hydrogels have been utilized for the healing of both acute and chronic wounds, which present unique biological microenvironments. In addition to these therapeutic applications, hydrogel bioprinting has been used to generate in vitro models of fibrosis in a variety of soft tissues such as the skin, heart, and liver, enabling high-throughput drug screening and tissue analysis at relatively low cost. As biological research begins to uncover the spatial biological features that underlie fibrosis and wound healing, bioprinting offers a powerful toolkit to recapitulate spatially defined pro-regenerative and anti-fibrotic cues for an array of translational applications.

Advances in polymer-based detection of environmental ibuprofen in wastewater.

Globally, ibuprofen is the third most consumed drug and its presence in the environment is a concern because little is known about its adverse effects on humans and aquatic life. Environmentalists have made monitoring and the detection of ibuprofen in biological and environmental matrices a priority. For the detection and monitoring of ibuprofen, sensors and biosensors have provided rapid analysis time, sensitivity, high-throughput screening, and real-time analysis. Researchers are increasingly seeking eco-friendly technology, and this has led to an interest in developing biodegradable, bioavailable, and non-toxic sensors, or biosensors. The integration of polymers into sensor systems has proven to significantly improve sensitivity, selectivity, and stability and minimize sample preparation using bioavailable and biodegradable polymers. This review provides a general overview of perspectives and trends of polymer-based sensors and biosensors for the detection of ibuprofen compared to non-polymer-based sensors.

Discovery and mechanism studies of a novel ATG4B inhibitor Ebselen by drug repurposing and its anti-colorectal cancer effects in mice

Cysteine protease ATG4B, a key autophagy protein, is an attractive target for colorectal cancer therapy. However, ATG4B inhibitors with higher efficiency, safety, and clear mechanism are still limited. In this study, we discovered ATG4B inhibitors based on the FDA-approved drug library through FRET-based high-throughput screening and gel-based analysis. Among the nine hits, compound Ebselen showed the most potent ATG4B inhibitory activity (IC50 = 189 nM) and exhibited controllable selectivity and structural optimizable possibility against ATG4A and caspases. We then performed mass spectrometry assay and cysteine mutations to confirm that Ebselen could covalently bind to ATG4B at Cys74. Moreover, Cys292 and Cys361 instead of Cys74 are responsible for the redox-oligomerization and efficient activity inhibition of ATG4B. Ultimately through cell culture and mouse xenograft tumor models, we established the impact of Ebselen on autophagy and tumor suppression via ATG4B inhibition other than apoptosis. These results suggest that old drug Ebselen as an ATG4B inhibitor through oxidative modification may be repurposed as a promising anti-colorectal cancer drug.

Using the Honey Bee (Apis mellifera L.) Cell Line AmE-711 to Evaluate Insecticide Toxicity.

One of the main contributors to poor productivity and elevated mortality of honey bee colonies globally is insecticide exposure. Whole-organism and colony-level studies have demonstrated the effects of insecticides on many aspects of honey bee biology and have also shown their interactions with pathogens. However, there is a need for in vitro studies using cell lines to provide greater illumination of the effects of insecticides on honey bee cellular and molecular processes. We used a continuous cell line established from honey bee embryonic tissues (AmE-711) in assays that enabled assessment of cell viability in response to insecticide exposure. We exposed AmE-711 cells to four formulations, each containing a different insecticide. Treatment of cells with the insecticides resulted in a concentration-dependent reduction in viability after a 24-h exposure, whereas long-term exposure (120 h) to sublethal concentrations had limited effects on viability. The 24-h exposure data allowed us to predict the half-maximal lethal concentration (LC50) for each insecticide using a four-parameter logistical model. We then exposed cells for 12 h to the predicted LC50 and observed changes in morphology that would indicate stress and death. Reverse transcription-quantitative polymerase chain reaction analysis corroborated changes in morphology: expression of a cellular stress response gene, 410087a, increased after an 18-h exposure to the predicted LC50. Demonstration of the effects of insecticides through use of AmE-711 provides a foundation for additional research addressing issues specific to honey bee toxicology and complements whole-organism and colony-level approaches. Moreover, advances in the use of AmE-711 in high-throughput screening and in-depth analysis of cell regulatory networks will promote the discovery of novel control agents with decreased negative impacts on honey bees. Environ Toxicol Chem 2023;42:88-99. Published 2022. This article is a U.S. Government work and is in the public domain in the USA. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Unravelling hub genes as potential therapeutic targets in lung cancer using integrated transcriptomic meta-analysis and in silico approach

Lung cancer (LC) is the leading cause of cancer-related deaths worldwide. Smoking has been identified as the main contributing cause of the disease’s development. The study aimed to identify the key genes in small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC), the two major types of LC. Meta-analysis was performed with two datasets GSE74706 and GSE149507 obtained from Gene Expression Omnibus (GEO). Both the datasets comprised samples from cancerous and adjacent non-cancerous tissues. Initially, differentially expressed genes (DEGs) were identified. To understand the underlying molecular mechanism of the identified genes, pathway enrichment, gene ontology (GO) and protein–protein interaction (PPI) analyses were done. A total of hub genes were identified which were subjected to mutation study analysis in LC patients using cBioPortal. These genes (i.e. AURKA, AURKB, KIF23, RACGAP1, KIF2C, KIF20A, CENPE, TPX2 and PRC1) have shown overexpression in LC patients and can be explored as potential candidates for prognostic biomarkers. TPX2 reported a maximum mutation of This was followed with high throughput screening and docking analysis to identify the potential drug candidates following competitive inhibition of the AURKA-TPX2 complex. Four compounds, CHEMBL431482, CHEMBL2263042, CHEMBL2385714, and CHEMBL1206617 were identified. The results signify that the selected 9 genes can be explored as biomarkers in disease prognosis and targeted therapy. Also, the identified 4 compounds can be further analyzed as promising therapeutic candidates. Communicated by Ramaswamy H. Sarma

An ascorbic acid-responsive chemo-chromic SERS sensing chip for synergistic dual-modal on-site analysis of alkaline phosphatase

This work designs an ascorbic acid (AA)-responsive chemo-chromic SERS sensing chip (C-SERS chip) for synergistic dual-modal on-site analysis. This chip can be easily prepared by immobilizing a new kind of core-shell nanoparticles named AuNSs-MBN@Ag@PB on flat filter membrane via vacuum filtration. The reduction of Prussian blue (PB) shell by AA can rapidly change the chip color and enhance SERS signal of 4-mercaptobenzonitrile (MBN), which leads to a synergistic dual-modal sensing strategy for rapid colorimetric screening and SERS quantification of AA-related analytes. Under optimal parameters, the C-SERS chip shows rapid colorimetric response and linear SERS response to AA concentration ranging from 0.5 to 100 μM. The limit of detection for AA is 0.24 μM. The good reproducibility, stability and robustness of the chip and its selectivity to AA demonstrate its practical application in food and biomedical analysis. Using alkaline phosphatase (ALP) as a model analyte, the proposed method with the help of 2-phosphate-L-ascorbic acid shows linear SERS response in the range of 0.5–100 U/L ALP. The excellent specificity, high accuracy, satisfactory recovery and convenient operation indicate the potential of the miniaturizable C-SERS chip in high-throughput on-site colorimetric screening and quantitative analysis by combining with a portable Raman spectrometer.