An automated fitting procedure and software for dose-response curves with multiphasic features

Ceftriaxone exerts antitumor effects in MYCN-driven retinoblastoma and neuroblastoma by targeting DDX3X for translation repression

MYCN proto-oncogene, bHLH transcription factor (MYCN) amplification is associated with aggressive retinoblastoma (RB) and neuroblastoma (NB) cancer recurrence that is resistant to chemotherapies. Therefore, there is an urgent need to identify new therapeutic tools. This study aimed to evaluate the potential repurposing of ceftriaxone for the treatment of MYCN-amplified RB and NB, based on the clinical observations that the drug was serendipitously found to decrease the volume of the MYCN-driven RB subtype. Using patient-derived tumor organoids and tumor cell lines, we demonstrated that ceftriaxone is a potent and selective growth inhibitor targeting MYCN-driven RB and NB cells. Profiling of drug-induced transcriptomic changes, cell-cycle progression, and apoptotic death indicated cell-cycle arrest and death of drug-treated MYCN-amplified tumor cells. Drug target identification, using an affinity-based proteomic and molecular docking approach, and functional studies of the target proteins revealed that ceftriaxone targeted DEAD-box helicase 3 X-linked (DDX3X), thereby inhibiting translation in MYCN-amplified tumors but not in MYCN-nonamplified cells. The data suggest the feasibility of repurposing ceftriaxone as an anticancer drug and provide insights into the mechanism of drug action, highlighting DDX3X as a potential target for treating MYCN-driven tumors.

Viridibacillus culture derived silver nanoparticles exert potent anticancer action in 2D and 3D models of lung cancer via mitochondrial depolarization-mediated apoptosis

Lung cancer is one of the most commonly occurring cancer types that accounts for almost 2 million cases per year. Its resistance to anticancer drugs, failure of new molecules in clinical trials, severe side-effects of current treatments, and its recurrence limit the success of anticancer therapies. Nanotherapeutic agents offer several advantages over conventional anticancer therapies, including improved retention in tumors, specificity, and anticancer effects at lower concentrations, hence reducing the side-effects. Here, we have explored the anticancer activity of silver nanoparticles synthesized in Viridibacillus sp. enriched culture medium for the first time. Such green nanoparticles, synthesized by biological systems, are superior to chemically synthesized ones in terms of their environmental footprint and production cost, and have one crucial advantage of excellent stability owing to their biological corona. To assess anticancer activity of these nanoparticles, we used conventional 2D cultured A549 cells as well as 3D spheroids of A549 cells. In both models of lung cancer, our silver nanoparticles diminished cell proliferation, arrested DNA synthesis, and showed a dose dependent cytotoxic effect. The nanoparticles damaged the DNA and mitochondrial structures in both A549 cells and A549 spheroids, leading to mitochondrial depolarization and increased cell permeability. Low lethal median doses (LD50) for 2D cultured A549 cells (1 μg/ml) and for A549 spheroids (13 μg/ml) suggest that our nanoparticles are potent anticancer agents. We also developed in vitro tumor progression model and in vitro tumor size model using 3D spheroids to test anticancer potential of our nanoparticles which otherwise would require longer experimental duration along with large number of animals and trained personnel. In these models, our nanoparticles showed strong dose dependent anticancer activity. In case of in vitro tumor progression model, the A549 cells failed to form tight spheroidal mass and showed increased dead cell fraction since day 1 as compared to control. On the other hand, in case of in vitro tumor size model, the 4 and 8 μg/ml nanoparticle treatment led to reduction in spheroid size from 615 ± 53 μm to 440 ± 45 μm and 612 ± 44 μm to 368 ± 62 μm respectively, within the time span of 3 days post treatment. We believe that use of such novel experimental models offers excellent and fast alternative to in vivo studies, and to the best of our knowledge, this is the first report that gives proof-of-concept for use of such novel in vitro cancer models to test anticancer agents such as Viridibacilli culture derived silver nanoparticles. Based on our results, we propose that these nanoparticles offer an interesting alternative for anticancer therapies, especially if they can be combined with classical anticancer drugs.

Translational modeling-based evidence for enhanced efficacy of standard-of-care drugs in combination with anti-microRNA-155 in non-small-cell lung cancer

Elevated microRNA-155 (miR-155) expression in non-small-cell lung cancer (NSCLC) promotes cisplatin resistance and negatively impacts treatment outcomes. However, miR-155 can also boost anti-tumor immunity by suppressing PD-L1 expression. We developed a multiscale mechanistic model, calibrated with in vivo data and then extrapolated to humans, to investigate the therapeutic effects of nanoparticle-delivered anti-miR-155 in NSCLC, alone or in combination with standard-of-care drugs. Model simulations and analyses of the clinical scenario revealed that monotherapy with anti-miR-155 at a dose of 2.5 mg/kg administered once every three weeks has substantial anti-cancer activity. It led to a median progression-free survival (PFS) of 6.7 months, which compared favorably to cisplatin and immune checkpoint inhibitors. Further, we explored the combinations of anti-miR-155 with standard-of-care drugs, and found strongly synergistic two- and three-drug combinations. A three-drug combination of anti-miR-155, cisplatin, and pembrolizumab resulted in a median PFS of 13.1 months, while a two-drug combination of anti-miR-155 and cisplatin resulted in a median PFS of 11.3 months, which emerged as a more practical option due to its simple design and cost-effectiveness. Our analyses also provided valuable insights into unfavorable dose ratios for drug combinations, highlighting the need for optimizing dose regimen to prevent antagonistic effects. Thus, this work bridges the gap between preclinical development and clinical translation of anti-miR-155 and unravels the potential of anti-miR-155 combination therapies in NSCLC.

How do biomarkers dance? Specific moves of defense and damage biomarkers for biological interpretation of dose-response model trends

Omics studies are currently increasingly used in ecotoxicology to highlight the induction of known or novel biomarkers when organisms are exposed to contaminants. Although it is virtually impossible to identify all biomarkers from all organisms, biomarkers can be grouped as defense or damage biomarkers, exhibiting a limited number of response trends. Our working hypothesis is that defense and damage biomarkers follow different dose-response patterns. A meta-analysis of 156 articles and 2595 observations of dose-response curves of defense and damage biomarkers was carried out in order to characterize the response trends of these biological parameters in a large panel of living organisms (18 phyla) exposed to inorganic or organic contaminants (176 in total). Using multinomial logistic regression models, defense biomarkers were found to describe biphasic responses (bell- and U-shaped) to a greater extent (2.5 times) than damage biomarkers. In contrast, damage biomarkers varied mainly monotonically (decreasing or increasing), representing 85% of the observations. Neither the nature of the contaminant nor the type of organisms belonging to 4 kingdoms, influence these specific responses. This result suggests that cellular defense and damage mechanisms are not specific to stressors and are conserved throughout life. Trend analysis of dose-response models as a biological interpretation of biomarkers could thus be a valuable way to exploit large omics datasets.

Experimental and data analysis advances in thermal proteome profiling

Method development for mass spectrometry (MS)-based thermal shift proteomic assays have advanced to probe small molecules with known and unknown protein-ligand interaction mechanisms and specificity, which is predominantly used in characterization of drug-protein interactions. In the discovery of target and off-target protein-ligand interactions, a thorough investigation of method development and their impact on the sensitivity and accuracy of protein-small molecule and protein-protein interactions is warranted. In this review, we discuss areas of improvement at each stage of thermal proteome profiling data analysis that includes processing of MS-based data, method development, and their effect on the overall quality of thermal proteome profiles. We also overview the optimization of experimental strategies and prioritization of an increased number of independent biological replicates over the number of evaluated temperatures.

Toxicokinetics of the Antidepressant Fluoxetine and Its Active Metabolite Norfluoxetine in Caenorhabditis elegans and Their Comparative Potency

The nematode Caenorhabditis elegans is a valuable model for ecotoxicological research, yet limited attention has been given to understanding how it absorbs, distributes, metabolizes, and excretes chemicals. This is crucial for C. elegans because the organism is known to have strong uptake barriers that are known to be susceptible to potential confounding effects of the presence of Escherichia coli as a food source. One frequently studied compound in C. elegans is the antidepressant fluoxetine, which has an active metabolite norfluoxetine. In this study, we evaluated the toxicokinetics and relative potency of norfluoxetine and fluoxetine in chemotaxis and activity tests. Toxicokinetics experiments were conducted with varying times, concentrations of fluoxetine, and in the absence or presence of E. coli, simulated with a one-compartment model. Our findings demonstrate that C. elegans can take up fluoxetine and convert it into norfluoxetine. Norfluoxetine proved slightly more potent and had a longer elimination half-life. The bioconcentration factor, uptake, and elimination rate constants depended on exposure levels, duration, and the presence of E. coli in the exposure medium. These findings expand our understanding of toxicokinetic modeling in C. elegans for different exposure scenarios, underlining the importance of considering norfluoxetine formation in exposure and bioactivity assessments of fluoxetine.

The hormesis principle of neuroplasticity and neuroprotection

Animals live in habitats fraught with a range of environmental challenges to their bodies and brains. Accordingly, cells and organ systems have evolved stress-responsive signaling pathways that enable them to not only withstand environmental challenges but also to prepare for future challenges and function more efficiently. These phylogenetically conserved processes are the foundation of the hormesis principle, in which single or repeated exposures to low levels of environmental challenges improve cellular and organismal fitness and raise the probability of survival. Hormetic principles have been most intensively studied in physical exercise but apply to numerous other challenges known to improve human health (e.g., intermittent fasting, cognitive stimulation, and dietary phytochemicals). Here we review the physiological mechanisms underlying hormesis-based neuroplasticity and neuroprotection. Approaching natural resilience from the lens of hormesis may reveal novel methods for optimizing brain function and lowering the burden of neurological disorders.

Enemies or Allies? Hormetic and Apparent Non-Dose-Dependent Effects of Natural Bioactive Antioxidants in the Treatment of Inflammation

This review aims to analyze the emerging number of studies on biological media that describe the unexpected effects of different natural bioactive antioxidants. Hormetic effects, with a biphasic response depending on the dose, or activities that are apparently non-dose-dependent, have been described for compounds such as resveratrol, curcumin, ferulic acid or linoleic acid, among others. The analysis of the reported studies confirms the incidence of these types of effects, which should be taken into account by researchers, discarding initial interpretations of imprecise methodologies or measurements. The incidence of these types of effects should enhance research into the different mechanisms of action, particularly those studied in the field of basic research, that will help us understand the causes of these unusual behaviors, depending on the dose, such as the inactivation of the signaling pathways of the immune defense system. Antioxidative and anti-inflammatory activities in biological media should be addressed in ways that go beyond a mere statistical approach. In this work, some of the research pathways that may explain the understanding of these activities are revised, paying special attention to the ability of the selected bioactive compounds (curcumin, resveratrol, ferulic acid and linoleic acid) to form metal complexes and the activity of these complexes in biological media.

Assessment of nonlinear dose-response relationships via nonparametric regression

We propose a simple approach to assess whether a nonlinear parametric model is appropriate to depict the dose-response relationships and whether two parametric models can be applied to fit a dataset via nonparametric regression. The proposed approach can compensate for the ANOVA, which is sometimes conservative, and is very easy to implement. We illustrate the performance by analyzing experimental examples and a small simulation study.

Quantitative and Standardized Pseudovirus Neutralization Assay for COVID-19

COVID-19 is a global pandemic caused by the highly infectious SARS-CoV-2 virus. Efforts to combat SARS-CoV-2 infection include mass vaccination and development of monoclonal and convalescent plasma therapeutics that require precise measurements of correlative, functional neutralizing antibodies that prevent virus infection. Developing rapid, safe, easy-to-use, and high-quality neutralization assays are essential for the success of the massive effort. Here, we developed a vesicular stomatitis virus-based neutralization assay that was capable of quantifying varying degrees of neutralization in patient serum samples. This assay has two detection readouts, flow cytometry and live cell imaging. The two readout methods produced consistent values of all 50% neutralization titers, further enhancing measurement confidence on the assay. Moreover, the use of available reference standards such as the World Health Organization International Standard (NIBSC code 20/136) enables quantification and standardization of the pseudovirus neutralization assay with neutralizing antibody titers measured in International Units/mL. Quantitative and standardized neutralization assays are critical for reliable efficacy evaluation and comparison of numerous vaccines and therapeutics.

Exploring the Safety of Pllans-II and Antitumoral Potential of Its Recombinant Isoform in Cervical Cancer Therapy

The antitumor potential of proteins from snake venoms has been studied in recent decades, and evidence has emerged that phospholipases A2 can selectively attack cells of various types of tumors. Previous results have shown that phospholipase A2 "Pllans-II," isolated from Porthidium lansbergii lansbergii snake venom, displayed antitumoral activity on cervical cancer and did not alter the viability of non-tumorigenic cells. However, until now, there was no evidence of its safety at the local and systemic levels, nor had experiments been developed to demonstrate that its production using recombinant technology allows us to obtain a molecule with effects similar to those generated by native phospholipase. Thus, we evaluated the impact caused by Pllans-II on murine biomodels, determining whether it induced local hemorrhage or increased pro-inflammatory and liver damage markers and histological alterations in the liver and kidneys. Additionally, the protein was produced using recombinant technology using a pET28a expression vector and the BL21 (DE3) Escherichia coli strain. Equally, its enzymatic activity and anticancer effect were evaluated on cervical cancer lines such as HeLa and Ca Ski. The results demonstrated that Pllans-II did not generate hemorrhagic activity, nor did it increase the pro-inflammatory cytokines IL-6, IL-1B, or TNF-α at doses of 3.28, 1.64, and 0.82 mg/kg. There was also no evidence of organ damage, and only ALT and AST increased in mild levels at the two highest concentrations. Additionally, the recombinant version of Pllans-II showed conservation in its catalytic activity and the ability to generate death in HeLa and Ca Ski cells (42% and 23%, respectively). These results demonstrate the innocuity of Pllans-II at the lowest dose and constitute an advance in considering a molecule produced using recombinant technology a drug candidate for selective attacks against cervical cancer.

Delicate plasticity: Maladaptive responses to fish predation risk in Daphnia magna caused by sertraline pollution

An emerging environmental pollutant may have a greater impact on phenotypic plasticity than its direct toxicity, causing maladaptive responses of organisms to their current environment. To better understand such ecological risks, we proposed a delicate plasticity hypothesis: if an emerging stressor acts on the fundamental processes underlying a specific adaptive plastic response, it is more likely to pose high risks to the phenotypic plasticity. Endocrine regulation is one of the critical processes of plasticity and is becoming a target for emerging pollutants. To test this hypothesis, we measured individual traits and the expression of endocrine-related genes in Daphnia magna in response to fish predation risk under exponentially increasing concentrations of the antidepressant sertraline, a selective serotonin reuptake inhibitor. The results showed that sertraline impaired most of the defense responses of D. magna at concentrations lower than the effective concentrations of its direct toxicity. The high risks of sertraline on inducible defenses were also visually reflected in the relationships between toxicity and plasticity strength, that is, most of the defense responses exponentially decayed with an increase in sertraline toxicity. In addition, the expression of genes involved in serotonin synthesis was significantly correlated with the expression of other endocrine-related genes and with changes in morphological traits. These results revealed that environmental sertraline pollution could disturb endocrine regulation and cause high risks to inducible defenses of D. magna, providing evidence supporting the delicate plasticity hypothesis.

CurveCurator: a recalibrated F-statistic to assess, classify, and explore significance of dose-response curves

Dose-response curves are key metrics in pharmacology and biology to assess phenotypic or molecular actions of bioactive compounds in a quantitative fashion. Yet, it is often unclear whether or not a measured response significantly differs from a curve without regulation, particularly in high-throughput applications or unstable assays. Treating potency and effect size estimates from random and true curves with the same level of confidence can lead to incorrect hypotheses and issues in training machine learning models. Here, we present CurveCurator, an open-source software that provides reliable dose-response characteristics by computing p-values and false discovery rates based on a recalibrated F-statistic and a target-decoy procedure that considers dataset-specific effect size distributions. The application of CurveCurator to three large-scale datasets enables a systematic drug mode of action analysis and demonstrates its scalable utility across several application areas, facilitated by a performant, interactive dashboard for fast data exploration.

Pllans-II: Unveiling the Action Mechanism of a Promising Chemotherapeutic Agent Targeting Cervical Cancer Cell Adhesion and Survival Pathways

Despite advances in chemotherapeutic drugs used against cervical cancer, available chemotherapy treatments adversely affect the patient's quality of life. For this reason, new molecules from natural sources with antitumor potential and few side effects are required. In previous research, Pllans-II, a phospholipase A2 type-Asp49 from Porthidium lansbergii lansbergii snake venom, has shown selective attack against the HeLa and Ca Ski cervical cancer cell lines. This work suggests that the cytotoxic effect generated by Pllans-II on HeLa cells is triggered without affecting the integrity of the cytoplasmic membrane or depolarizing the mitochondrial membranes. The results allow us to establish that cell death in HeLa is related to the junction blockage between α5β1 integrins and fibronectin of the extracellular matrix. Pllans-II reduces the cells' ability of adhesion and affects survival and proliferation pathways mediated by intracellular communication with the external environment. Our findings confirmed Pllans-II as a potential prototype for developing a selective chemotherapeutic drug against cervical cancer.

Monoclonal Antibodies as SARS-CoV-2 Serology Standards: Experimental Validation and Broader Implications for Correlates of Protection

COVID-19 has highlighted challenges in the measurement quality and comparability of serological binding and neutralization assays. Due to many different assay formats and reagents, these measurements are known to be highly variable with large uncertainties. The development of the WHO international standard (WHO IS) and other pool standards have facilitated assay comparability through normalization to a common material but does not provide assay harmonization nor uncertainty quantification. In this paper, we present the results from an interlaboratory study that led to the development of (1) a novel hierarchy of data analyses based on the thermodynamics of antibody binding and (2) a modeling framework that quantifies the probability of neutralization potential for a given binding measurement. Importantly, we introduced a precise, mathematical definition of harmonization that separates the sources of quantitative uncertainties, some of which can be corrected to enable, for the first time, assay comparability. Both the theory and experimental data confirmed that mAbs and WHO IS performed identically as a primary standard for establishing traceability and bridging across different assay platforms. The metrological anchoring of complex serological binding and neuralization assays and fast turn-around production of an mAb reference control can enable the unprecedented comparability and traceability of serological binding assay results for new variants of SARS-CoV-2 and immune responses to other viruses.

A Comparative Study of the Inhibitory Effect of Some Flavonoids and a Conjugate of Taxifolin with Glyoxylic Acid on the Oxidative Burst of Neutrophils

During the storage, processing, and digestion of flavonoid-rich foods and beverages, a condensation of flavonoids with toxic carbonyl compounds occurs. The effect of the resulting products on cells remains largely unknown. The aim of the present study was to evaluate the effects of quercetin, taxifolin, catechin, eriodictyol, hesperetin, naringenin, and a condensation product of taxifolin with glyoxylic acid on the oxidative burst of neutrophils. It was found that the flavonoids and the condensation product inhibited the total production of ROS. Flavonoids decreased both the intra and extracellular ROS production. The condensation product had no effect on intracellular ROS production but effectively inhibited the extracellular production of ROS. Thus, the condensation of flavonoids with toxic carbonyl compounds may lead to the formation of compounds exhibiting potent inhibitory effects on the oxidative burst of neutrophils. The data also suggest that, during these reactions, the influence of a fraction of flavonoids and their polyphenolic derivatives on cellular functions may change. On the whole, the results of the study provide a better understanding of the effects of polyphenols on human health. In addition, these results reveal the structure-activity relationship of these polyphenols and may be useful in a search for new therapeutic agents against diseases associated with oxidative stress.

Inclusion of Control Data in Fits to Concentration-Response Curves Improves Estimates of Half-Maximal Concentrations

Concentration-response curves, in which the effect of varying the concentration on the response of an assay is measured, are widely used to evaluate biological effects of chemical compounds. While National Center for Advancing Translational Sciences guidelines specify that readouts should be normalized by the controls, recommended statistical analyses do not explicitly fit to the control data. Here, we introduce a nonlinear regression procedure based on maximum likelihood estimation that determines parameters for the classical Hill equation by fitting the model to both the curve and the control data. Simulations show that the proposed procedure provides more precise parameters compared with previously prescribed practices. Analysis of enzymatic inhibition data from the COVID Moonshot demonstrates that the proposed procedure yields a lower asymptotic standard error for estimated parameters. Benefits are most evident in the analysis of the incomplete curves. We also find that Lenth's outlier detection method appears to determine parameters more precisely.

Combined Dextran-Graft-Polyacrylamide/Zinc Oxide Nanocarrier for Effective Anticancer Therapy in vitro

Introduction

Cancer chemotherapy faces two major challenges - high toxicity of active substances and tumor resistance to drugs. Low toxic nanocarriers in combination with anticancer agents can significantly increase the effectiveness of therapy. Modern advances in nanotechnology make it easy to create materials with the necessary physical and chemical properties.

Methods

Two hybrid nanosystems of dextran-polyacrylamide/ zinc oxide nanoparticles (D-PAA/ZnO NPs) were synthesized in aqueous solution with zinc sulphate (D-PAA/ZnO NPs (SO42-)) and zinc acetate (D-PAA/ZnO NPs (-OAc)). The light absorption, fluorescence, dynamic light scattering and transmission electron microscopy for nanocomposite characterization were used. MTT, neutral red uptake and scratch assays were selected as fibroblasts cytotoxicity assays. Cytotoxicity was tested in vitro for normal fibroblasts, MAEC, prostate (LNCaP, PC-3, DU-145) and breast (MDA-MB-231, MCF-7) cancer cells lines. Immunocytochemical methods were used for detection of Ki-67, p53, Bcl-2, Bax, e-cadherin, N-cadherin and CD44 expression. Acridine orange was used to detect morphological changes in cells.

Results

The radius of ZnO NPs (SO42-) was 1.5 nm and ZnO NPs (-OAc) was 2 nm. The nanosystems were low-toxic to fibroblasts, MAEC. Cells in the last stages of apoptosis with the formation of apoptotic bodies were detected for all investigated cancer cell lines. Proapoptotic proteins expression in cancer cells indicates an apoptotic death. Increased expression of E-cadherin and N-cadherin was registered for cancer cells line LNCaP, PC-3, DU-145 and MCF-7 after 48 h incubation with D-PAA/ZnO NPs (SO42-).

Conclusion

The nanosystems were low-toxic to fibroblasts, MAEC. The D-PAA/ZnO NPs nanosystem synthesized using zinc sulphate demonstrates high cytotoxicity due to destruction of various types of cancer cells in vitro and potentially increases adhesion between cells. Thus, our findings indicate the selective cytotoxicity of D-PAA/ZnO NPs against cancer cells and can be potentially used for cancer treatment.

Relationship between brain iron dynamics and blood-brain barrier function during childhood: a quantitative magnetic resonance imaging study

BACKGROUND

Mounting evidence suggests that the blood-brain barrier (BBB) plays an important role in the regulation of brain iron homeostasis in normal brain development, but these imaging profiles remain to be elucidated. We aimed to establish a relationship between brain iron dynamics and BBB function during childhood using a combined quantitative magnetic resonance imaging (MRI) to depict both physiological systems along developmental trajectories.

METHODS

In this single-center prospective study, consecutive outpatients, 2-180 months of age, who underwent brain MRI (3.0-T scanner; Ingenia; Philips) between January 2020 and January 2021, were included. Children with histories of preterm birth or birth defects, abnormalities on MRI, and diagnoses that included neurological diseases during follow-up examinations through December 2022 were excluded. In addition to clinical MRI, quantitative susceptibility mapping (QSM; iron deposition measure) and diffusion-prepared pseudo-continuous arterial spin labeling (DP-pCASL; BBB function measure) were acquired. Atlas-based analyses for QSM and DP-pCASL were performed to investigate developmental trajectories of regional brain iron deposition and BBB function and their relationships.

RESULTS

A total of 78 children (mean age, 73.8 months ± 61.5 [SD]; 43 boys) were evaluated. Rapid magnetic susceptibility progression in the brain (Δsusceptibility value) was observed during the first two years (globus pallidus, 1.26 ± 0.18 [× 10- 3 ppm/month]; substantia nigra, 0.68 ± 0.16; thalamus, 0.15 ± 0.04). The scattergram between the Δsusceptibility value and the water exchange rate across the BBB (kw) divided by the cerebral blood flow was well fitted to the sigmoidal curve model, whose inflection point differed among each deep gray-matter nucleus (globus pallidus, 2.96-3.03 [mL/100 g]-1; substantia nigra, 3.12-3.15; thalamus, 3.64-3.67) in accordance with the regional heterogeneity of brain iron accumulation.

CONCLUSIONS

The combined quantitative MRI study of QSM and DP-pCASL for pediatric brains demonstrated the relationship between brain iron dynamics and BBB function during childhood.

TRIAL REGISTRATION

UMIN Clinical Trials Registry identifier: UMIN000039047, registered January 6, 2020.

Challenges and Opportunities in Developing Targeted Therapies for Triple Negative Breast Cancer

Triple negative breast cancer (TNBC) is a heterogeneous group of breast cancers characterized by their lack of estrogen receptors, progesterone receptors, and the HER2 receptor. They are more aggressive than other breast cancer subtypes, with a higher mean tumor size, higher tumor grade, the worst five-year overall survival, and the highest rates of recurrence and metastasis. Developing targeted therapies for TNBC has been a major challenge due to its heterogeneity, and its treatment still largely relies on surgery, radiation therapy, and chemotherapy. In this review article, we review the efforts in developing targeted therapies for TNBC, discuss insights gained from these efforts, and highlight potential opportunities going forward. Accumulating evidence supports TNBCs as multi-driver cancers, in which multiple oncogenic drivers promote cell proliferation and survival. In such multi-driver cancers, targeted therapies would require drug combinations that simultaneously block multiple oncogenic drivers. A strategy designed to generate mechanism-based combination targeted therapies for TNBC is discussed.

Quantitative Attribution of the Protective Effects of Aminosterols against Protein Aggregates to Their Chemical Structures and Ability to Modulate Biological Membranes

Natural aminosterols are promising drug candidates against neurodegenerative diseases, like Alzheimer and Parkinson, and one relevant protective mechanism occurs via their binding to biological membranes and displacement or binding inhibition of amyloidogenic proteins and their cytotoxic oligomers. We compared three chemically different aminosterols, finding that they exhibited different (i) binding affinities, (ii) charge neutralizations, (iii) mechanical reinforcements, and (iv) key lipid redistributions within membranes of reconstituted liposomes. They also had different potencies (EC₅₀) in protecting cultured cell membranes against amyloid-β oligomers. A global fitting analysis led to an analytical equation describing quantitatively the protective effects of aminosterols as a function of their concentration and relevant membrane effects. The analysis correlates aminosterol-mediated protection with well-defined chemical moieties, including the polyamine group inducing a partial membrane-neutralizing effect (79 ± 7%) and the cholestane-like tail causing lipid redistribution and bilayer mechanical resistance (21 ± 7%), linking quantitatively their chemistry to their protective effects on biological membranes.

Improving In Vitro Detection of Sensitization to Lipid Transfer Proteins: A New Molecular Multiplex IgE Assay

SCOPE

LTP-syndrome is characterized by sensitization (IgE) to multiple non-specific lipid transfer proteins (nsLTPs) with a variable clinical outcome. The treatment is primarily based on offending food avoidance. However, the determination of Pru p 3-specific IgE is currently the main diagnostic tool to assess sensitization to nsLTPs. Herein, the study evaluates improvement of LTP-syndrome diagnosis and clinical management using a new IgE multiplex-immunoblot assay with a high diversity of food nsLTPs.

METHODS AND RESULTS

An EUROLINE-LTP strip with 28 recombinant nsLTPs from 18 allergenic sources is designed. In total the study investigates 38 patients with LTP-syndrome and compares results from the nsLTPs (LTP-strip) with the respective food extracts of Prick-by-prick (PbP) testing. The agreement exceeds 70% for most nsLTPs, e.g., Pru p 3 (100%), Mal d 3 (97%), Pru av 3 (89%), Pha v 3 isoforms (87%/84%), Ara h 9 (82%), Cor a 8 (82%), and Jug r 3 (82%). The functionality and allergenic relevance of nine recombinant nsLTPs are proven by Basophil activation testing (BAT).

CONCLUSIONS

The new IgE multiplex-immunoblot nsLTP assay shows a good diagnostic performance allowing culprit food assessment. Negative results from LTP-strip may indicate potentially tolerable foods, improving diet intervention and patients' quality of life.

Role of Residual Monomers in the Manifestation of (Cyto)toxicity by Polystyrene Microplastic Model Particles

Polystyrene (PS) is an important model polymer for the investigation of effects of microplastic (MP) and nanoplastic (NP) particles on living systems. Aqueous dispersions of PS MP or NP contain residual monomers of styrene. In consequence, it is not clear if the effects observed in standard (cyto)toxicity studies are evoked by the polymer (MP/NP) particle or by residual monomers. We addressed that question by comparing standard PS model particle dispersions with in-house synthesized PS particle dispersions. We proposed a rapid purification method of PS particle dispersions by dialysis against mixed solvents and developed a simple method of UV-vis spectrometry to detect residual styrene in the dispersions. We found that standard PS model particle dispersions, which contain residual monomers, exerted a low but significant cytotoxicity on mammalian cells, while the in-house synthesized PS, after rigorous purification to reduce the styrene content, did not. However, the PS particles per se but not the residual styrene in both PS particle dispersions resulted in immobilization of Daphnia. Only by using freshly monomer-depleted particles, will it be possible in the future to assess the (cyto)toxicities of PS particles, avoiding an otherwise not controllable bias effect of the monomer.

Four PQQ-Dependent Alcohol Dehydrogenases Responsible for the Oxidative Detoxification of Deoxynivalenol in a Novel Bacterium Ketogulonicigenium vulgare D3_3 Originated from the Feces of Tenebrio molitor Larvae

Deoxynivalenol (DON) is frequently detected in cereals and cereal-based products and has a negative impact on human and animal health. In this study, an unprecedented DON-degrading bacterial isolate D3_3 was isolated from a sample of Tenebrio molitor larva feces. A 16S rRNA-based phylogenetic analysis and genome-based average nucleotide identity comparison clearly revealed that strain D3_3 belonged to the species Ketogulonicigenium vulgare. This isolate D3_3 could efficiently degrade 50 mg/L of DON under a broad range of conditions, such as pHs of 7.0-9.0 and temperatures of 18-30 °C, as well as during aerobic or anaerobic cultivation. 3-keto-DON was identified as the sole and finished DON metabolite using mass spectrometry. In vitro toxicity tests revealed that 3-keto-DON had lower cytotoxicity to human gastric epithelial cells and higher phytotoxicity to Lemna minor than its parent mycotoxin DON. Additionally, four genes encoding pyrroloquinoline quinone (PQQ)-dependent alcohol dehydrogenases in the genome of isolate D3_3 were identified as being responsible for the DON oxidation reaction. Overall, as a highly potent DON-degrading microbe, a member of the genus Ketogulonicigenium is reported for the first time in this study. The discovery of this DON-degrading isolate D3_3 and its four dehydrogenases will allow microbial strains and enzyme resources to become available for the future development of DON-detoxifying agents for food and animal feed.

In-silico clearing approach for deep refractive index tomography by partial reconstruction and wave-backpropagation

Refractive index (RI) is considered to be a fundamental physical and biophysical parameter in biological imaging, as it governs light-matter interactions and light propagation while reflecting cellular properties. RI tomography enables volumetric visualization of RI distribution, allowing biologically relevant analysis of a sample. However, multiple scattering (MS) and sample-induced aberration (SIA) caused by the inhomogeneity in RI distribution of a thick sample make its visualization challenging. This paper proposes a deep RI tomographic approach to overcome MS and SIA and allow the enhanced reconstruction of thick samples compared to that enabled by conventional linear-model-based RI tomography. The proposed approach consists of partial RI reconstruction using multiple holograms acquired with angular diversity and their backpropagation using the reconstructed partial RI map, which unambiguously reconstructs the next partial volume. Repeating this operation efficiently reconstructs the entire RI tomogram while suppressing MS and SIA. We visualized a multicellular spheroid of diameter 140 µm within minutes of reconstruction, thereby demonstrating the enhanced deep visualization capability and computational efficiency of the proposed method compared to those of conventional RI tomography. Furthermore, we quantified the high-RI structures and morphological changes inside multicellular spheroids, indicating that the proposed method can retrieve biologically relevant information from the RI distribution. Benefitting from the excellent biological interpretability of RI distributions, the label-free deep visualization capability of the proposed method facilitates a noninvasive understanding of the architecture and time-course morphological changes of thick multicellular specimens.

The Influence of Liquid Menisci on Nanoparticle Dosimetry in Submerged Cells

Understanding the interaction between cells and nanoparticles (NPs) is vital to understand the hazard associated with nanoparticles. This requires quantifying and interpreting dose-response relationships. Experiments with cells cultured in vitro and exposed to particle dispersions mainly rely on mathematical models that estimate the received nanoparticle dose. However, models need to consider that aqueous cell culture media wets the inner surface of hydrophilic open wells, which results in a curved liquid-air interface called the meniscus. Here the impact of the meniscus on nanoparticle dosimetry is addressed in detail. Experiments and build an advanced mathematical model, to demonstrate that the presence of the meniscus may bring about systematic errors that must be considered to advance reproducibility and harmonization is presented. The script of the model is co-published and can be adapted to any experimental setup. Finally, simple and practical solutions to this problem, such as covering the air-liquid interface with a permeable lid or soft rocking of the cell culture well plate is proposed.

Phenotypic deconvolution in heterogeneous cancer cell populations using drug-screening data

Tumor heterogeneity is an important driver of treatment failure in cancer since therapies often select for drug-tolerant or drug-resistant cellular subpopulations that drive tumor growth and recurrence. Profiling the drug-response heterogeneity of tumor samples using traditional genomic deconvolution methods has yielded limited results, due in part to the imperfect mapping between genomic variation and functional characteristics. Here, we leverage mechanistic population modeling to develop a statistical framework for profiling phenotypic heterogeneity from standard drug-screen data on bulk tumor samples. This method, called PhenoPop, reliably identifies tumor subpopulations exhibiting differential drug responses and estimates their drug sensitivities and frequencies within the bulk population. We apply PhenoPop to synthetically generated cell populations, mixed cell-line experiments, and multiple myeloma patient samples and demonstrate how it can provide individualized predictions of tumor growth under candidate therapies. This methodology can also be applied to deconvolution problems in a variety of biological settings beyond cancer drug response.

Anti-human immunodeficiency virus-1 activity of MoMo30 protein isolated from the traditional African medicinal plant Momordica balsamina

BACKGROUND

Plants are used in traditional healing practices of many cultures worldwide. Momordica balsamina is a plant commonly used by traditional African healers as a part of a treatment for HIV/AIDS. It is typically given as a tea to patients with HIV/AIDS. Water-soluble extracts of this plant were found to contain anti-HIV activity.

METHODS

We employed cell-based infectivity assays, surface plasmon resonance, and a molecular-cell model of the gp120-CD4 interaction to study the mechanism of action of the MoMo30-plant protein. Using Edman degradation results of the 15 N-terminal amino acids, we determined the gene sequence of the MoMo30-plant protein from an RNAseq library from total RNA extracted from Momordica balsamina.

RESULTS

Here, we identify the active ingredient of water extracts of the leaves of Momordica balsamina as a 30 kDa protein we call MoMo30-plant. We have identified the gene for MoMo30 and found it is homologous to a group of plant lectins known as Hevamine A-like proteins. MoMo30-plant is distinct from other proteins previously reported agents from the Momordica species, such as ribosome-inactivating proteins such as MAP30 and Balsamin. MoMo30-plant binds to gp120 through its glycan groups and functions as a lectin or carbohydrate-binding agent (CBA). It inhibits HIV-1 at nanomolar levels and has minimal cellular toxicity at inhibitory levels.

CONCLUSIONS

CBAs like MoMo30 can bind to glycans on the surface of the enveloped glycoprotein of HIV (gp120) and block entry. Exposure to CBAs has two effects on the virus. First, it blocks infection of susceptible cells. Secondly, MoMo30 drives the selection of viruses with altered glycosylation patterns, potentially altering their immunogenicity. Such an agent could represent a change in the treatment strategy for HIV/AIDS that allows a rapid reduction in viral loads while selecting for an underglycosylated virus, potentially facilitating the host immune response.

A Multiplex Molecular Cell-Based Sensor to Detect Ligands of PPARs: An Optimized Tool for Drug Discovery in Cyanobacteria

Cyanobacteria produce a wealth of secondary metabolites. Since these organisms attach fatty acids into molecules in unprecedented ways, cyanobacteria can serve as a novel source for bioactive compounds acting as ligands for Peroxisome Proliferator-Activated Receptors (PPAR). PPARs (PPARα, PPARβ/δ and PPARγ) are ligand-activated nuclear receptors, involved in the regulation of various metabolic and cellular processes, thus serving as potential drug targets for a variety of pathologies. Yet, given that PPARs' agonists can have pan-, dual- or isoform-specific action, some controversy has been raised over currently approved drugs and their side effects, highlighting the need for novel molecules. Here, we expand and validate a cell-based PPAR transactivation activity biosensor, and test it in a screening campaign to guide drug discovery. Biosensor upgrades included the use of different reporter genes to increase signal intensity and stability, a different promoter to modulate reporter gene expression, and multiplexing to improve efficiency. Sensor's limit of detection (LOD) ranged from 0.36-0.89 nM in uniplex and 0.89-1.35 nM in multiplex mode. In triplex mode, the sensor's feature screening, a total of 848 fractions of 96 cyanobacteria extracts were screened. Hits were confirmed in multiplex mode and in uniplex mode, yielding one strain detected to have action on PPARα and three strains to have dual action on PPARα and -β.

Contrasting dose response relationships of neuroactive antidepressants on the behavior of C. elegans

Antidepressant prescriptions are on a rise worldwide and this increases the concerns for the impacts of these pharmaceuticals on nontarget organisms. Antidepressants are neuroactive compounds that can affect organism's behavior. Behavior is a sensitive endpoint that may also propagate effects at a population level. Another interesting aspect of antidepressants is that they have shown to induce non-monotonic dose-response (NMDR) curves. While such NMDR relationships may have clear implications for the environmental risk, the resolution of current studies is often too coarse to be able to detect relevant NMDR. Therefore, the current study was performed into the behavioral effects (activity, feeding and chemotaxis) in Caenorhabditis elegans as the model organism of the selective serotonin reuptake inhibitors fluoxetine and sertraline and the acetylcholinesterase inhibiting pesticide chlorpyrifos, using a wide range of concentrations (ng/l to mg/l). In order to statistically examine the non-monotonicity, nonlinear regression models were applied to the results. The results showed a triphasic dose-response relationship for activity and chemotaxis after exposure to fluoxetine, but not to sertraline or chlorpyrifos. Effects of fluoxetine already occurred at low concentrations in the range of ng/l while sertraline only showed effects at concentrations in the μg/l range, similar to chlorpyrifos. The different responses between fluoxetine and sertraline, both SSRIs, indicate that response patterns may not always be extrapolated from chemicals with the same primary mode of action. The effects of fluoxetine at low concentrations, in a non-monotonic manner, confirm the relevance of examining such responses at low concentrations.

On the meta-analysis of hormetic effects

The evidence for hormetic responses with chemical effects at doses lower than the no-observed-adverse-effect-level (sub-NOAEL) is increasing, creating a need for meta-analyses of sub-NOAEL effects across studies. However, the distinct features of hormetic responses complicate the procedures of meta-analyses aiming to study sub-NOAEL, hormetic effects, and there is no standardized methodology to serve as a guideline. In this piece, a protocol is proposed, which covers the selection of more holistic keywords to be integrated into the literature search queries, the designation of control, and the identification of NOAEL (and thus sub-NOAEL dose responses). It also considers the selection of the response indicators and the incorporation of time and dose as sources of variation. This protocol can serve as a reference point for a harmonized and more robust methodology to meta-analyze sub-NOAEL effects of chemicals on living organisms.

Environmental pollution impacts: Are p values over-valued?

An examination revealed the dominance of the published literature of environmental science by p values. Meanwhile, the use of effect size has been neglected in publications reporting primary data, yet the size of effect is often more informative than p values inference in assessing the effects of pollution on living organisms, comparing susceptibility/resistance among organisms, and ranking pollutants according to their potency, among others. Statistical significance does not necessarily mean biological, practical, or scientific significance, and its use based on (often misinterpreted) p values reflects the average response or effect at average conditions based on an assumed linear model fit to the entire sample. However, pollution impacts and organismal responses are rarely characterized by linear and symmetric features, and dichotomous 'statistical significance' based on p values is inadequate to fully describe data and findings. Considering 'the fallacy of the average', variance, and differential response of different population percentiles in new studies would provide otherwise wasted biologically, practically, or scientifically significant information. Since p values often inform as to whether some findings warrant further examination, journals should consider mandating the reporting of effect sizes and confidence intervals, together with p values (should they be used), to provide more integrated information regarding pollution impacts. Moreover, replacing 'statistical significance' with language of evidence, especially in key components of publications, such as abstracts and conclusions, could help preventing potential misleading of the public and decision and policy makers.

Effects of Two Antiretroviral Drugs on the Crustacean Daphnia magna in River Water

Antiretroviral (ARVs) drugs are used to manage the human immunodeficiency virus (HIV) disease and are increasingly being detected in the aquatic environment. However, little is known about their effects on non-target aquatic organisms. Here, Daphnia magna neonates were exposed to Efavirenz (EFV) and Tenofovir (TFV) ARVs at 62.5–1000 µg/L for 48 h in river water. The endpoints assessed were mortality, immobilization, and biochemical biomarkers (catalase (CAT), glutathione S-transferase (GST), and malondialdehyde (MDA)). No mortality was observed over 48 h. Concentration- and time-dependent immobilization was observed for both ARVs only at 250–1000 µg/L after 48 h, with significant immobilization observed for EFV compared to TFV. Results for biochemical responses demonstrated that both ARVs induced significant changes in CAT and GST activities, and MDA levels, with effects higher for EFV compared to TFV. Biochemical responses were indicative of oxidative stress alterations. Hence, both ARVs could potentially be toxic to D. magna.

Analytical methods for assessing retinal cell coupling using cut-loading

Electrical coupling between retinal neurons contributes to the functional complexity of visual circuits. “Cut-loading” methods allow simultaneous assessment of cell-coupling between multiple retinal cell-types, but existing analysis methods impede direct comparison with gold standard direct dye injection techniques. In the current study, we both improved an existing method and developed two new approaches to address observed limitations. Each method of analysis was applied to cut-loaded dark-adapted Guinea pig retinae (n = 29) to assess coupling strength in the axonless horizontal cell type (‘a-type’, aHCs). Method 1 was an improved version of the standard protocol and described the distance of dye-diffusion (space constant). Method 2 adjusted for the geometric path of dye-transfer through cut-loaded cells and extracted the rate of dye-transfer across gap-junctions in terms of the coupling coefficient (k_j). Method 3 measured the diffusion coefficient (De) perpendicular to the cut-axis. Dye transfer was measured after one of five diffusion times (1–20 mins), or with a coupling inhibitor, meclofenamic acid (MFA) (50–500μM after 20 mins diffusion). The standard protocol fits an exponential decay function to the fluorescence profile of a specified retina layer but includes non-specific background fluorescence. This was improved by measuring the fluorescence of individual cell soma and excluding from the fit non-horizontal cells located at the cut-edge (p<0.001) (Method 1). The space constant (Method 1) increased with diffusion time (p<0.01), whereas Methods 2 (p = 0.54) and 3 (p = 0.63) produced consistent results across all diffusion times. Adjusting distance by the mean cell-cell spacing within each tissue reduced the incidence of outliers across all three methods. Method 1 was less sensitive to detecting changes induced by MFA than Methods 2 (p<0.01) and 3 (p<0.01). Although the standard protocol was easily improved (Method 1), Methods 2 and 3 proved more sensitive and generalisable; allowing for detailed assessment of the tracer kinetics between different populations of gap-junction linked cell networks and direct comparison to dye-injection techniques.

α-Hydroxylactams as Efficient Entries to Diversely Functionalized Ferrociphenols: Synthesis and Antiproliferative Activity Studies

The [ferrocene-ene-phenol] motif has been identified as the pharmacophore responsible for the anticancer activity of the family of ferrocene-based molecules coined ferrocifens, owing to its unique redox properties. The addition of imide entities to the historical ferrociphenol scaffold tremendously enhanced the cytotoxic activity of a large panel of cancer cell cultures and preliminary studies showed that the reduction of one of the carbonyl groups of the imide groups to the corresponding α-hydroxylactams only slightly affected the antiproliferative activity. As a continuation to these studies, we took advantage of the facile conversion of α-hydroxylactams to highly electrophilic N-acyliminium ions to graft various substituents to the imide motif of phthalimido ferrocidiphenol. Cell viability studies showed that the newly synthesized compounds showed diverse cytotoxic activities on two breast cancer cell lines, while only one compound was significantly less active on the non-tumorigenic cell line hTERT-RPE1.

Predictive approach of COVID-19 propagation via multiple-terms sigmoidal transition model

The COVID-19 pandemic with its new variants has severely affected the whole world socially and economically. This study presents a novel data analysis approach to predict the spread of COVID-19. SIR and logistic models are commonly used to determine the duration at the end of the pandemic. Results show that these well-known models may provide unrealistic predictions for countries that have pandemics spread with multiple peaks and waves. A new prediction approach based on the sigmoidal transition (ST) model provided better estimates than the traditional models. In this study, a multiple-term sigmoidal transition (MTST) model was developed and validated for several countries with multiple peaks and waves. This approach proved to fit the actual data better and allowed the spread of the pandemic to be accurately tracked. The UK, Italy, Saudi Arabia, and Tunisia, which experienced several peaks of COVID-19, were used as case studies. The MTST model was validated for these countries for the data of more than 500 days. The results show that the correlating model provided good fits with regression coefficients (R2) > 0.999. The estimated model parameters were obtained with narrow 95% confidence interval bounds. It has been found that the optimum number of terms to be used in the MTST model corresponds to the highest R², the least RMSE, and the narrowest 95% confidence interval having positive bounds.

Atmospheric Pb induced hormesis in the accumulator plant Tillandsia usneoides

While numerous studies reported hormesis in plants exposed to heavy metals, metals were commonly added in the growth substrate (e.g. soil or solution). The potential of heavy metals in the atmosphere to induce hormesis in plants, however, remains unknown. In this study, we exposed the widely-used accumulator plant Tillandsia usneoides to 10 atmospheric Pb concentrations (0-25.6 μg·m^-3) for 6 or 12 h. Three types of dose-response relationships between different response endpoints (biomarkers) and Pb concentrations were found for T. usneoides. The first was a monophasic dose response, in which the response increased linearly with increasing Pb concentrations, as seen for metallothionein (MT) content after a 6-h exposure. The second and dominating type was a biphasic-hormetic dose response, exhibited by malondialdehyde (MDA), superoxide anion radical (O₂^-), and superoxide dismutase (SOD) after 6 or 12 h of exposure and by glutathione (GSH) and MT content after 12 h of treatment. The third type was a triphasic dose response, as seen for leaf electric conductivity after 6 or 12 h of exposure and GSH after 6 h of exposure. This finding suggests that Pb inhibited the response of T. usneoides at very low concentrations, stimulated it at low-to-moderate concentrations, and inhibited it at higher concentrations. Our results demonstrate diverse adaptation mechanisms of plants to stress, in the framework of which alternating between up- and down-regulation of biomarkers is at play when responding to different levels of toxicants. The emergence of the triphasic dose response will further enhance the understanding of time-dependent hormesis.

Non-thermal plasma induces changes in aflatoxin production, devitalization, and surface chemistry of Aspergillus parasiticus

Non-thermal plasma (NTP) represents the fourth state of matter composed of neutral molecules, atoms, ions, radicals, and electrons. It has been used by various industries for several decades, but only recently NTPs have emerged in fields such as medicine, agriculture, and the food industry. In this work, we studied the effect of NTP exposure on aflatoxin production, conidial germination and mycelial vitality, morphological and surface changes of conidia and mycelium. When compared with colonies grown from untreated conidia, the colonies from NTP-treated conidia produced significantly higher levels of aflatoxins much earlier during development than colonies from untreated conidia. However, at the end of cultivation, both types of cultures yielded similar aflatoxin concentrations. The increase in the accumulation of aflatoxins was supported by high transcription levels of aflatoxin biosynthetic genes, which indicated a possibility that NTP treatment of conidia was having a longer-lasting effect on colony development and aflatoxins accumulation. NTP generated in the air at atmospheric pressure effectively devitalized Aspergillus parasiticus in conidia and hyphae within a few minutes of treatment. To describe devitalization kinetics, we applied Weibull and Hill models on sets of data collected at different exposure times during NTP treatment. The damage caused by NTP to hyphal cell wall structures was displayed by raptures visualized by scanning electron microscopy. Fourier transform infrared spectroscopy demonstrated that changes in cell envelope correlated with shifts in characteristic chemical bonds indicating dehydration, oxidation of lipids, proteins, and polysaccharides. Key points • Non-thermal plasma increases aflatoxin production shortly after treatment. • Non-thermal plasma rapidly devitalizes Aspergillus parasiticus. • Non-thermal plasma disrupts the cell surface and oxidizes biological components.

Computational Pipeline for Rational Drug Combination Screening in Patient-Derived Cells

In many complex diseases, such as cancers, resistance to monotherapies easily occurs, and longer-term treatment responses often require combinatorial therapies as next-line regimens. However, due to a massive number of possible drug combinations to test, there is a need for systematic and rational approaches to finding safe and effective drug combinations for each individual patient. This protocol describes an ecosystem of computational methods to guide high-throughput combinatorial screening that help experimental researchers to identify optimal drug combinations in terms of synergy, efficacy, and/or selectivity for further preclinical and clinical investigation. The methods are demonstrated in the context of combinatorial screening in primary cells of leukemia patients, where the translational aim is to identify drug combinations that show not only high synergy but also maximal cancer-selectivity. The mechanism-agnostic and cost-effective computational methods are widely applicable to various cancer types, which are amenable to drug testing, as the computational methods take as input only the phenotypic measurements of a subset of drug combinations, without requiring target information or genomic profiles of the patient samples.

Attomole-per Cell Atomic Mass Spectrometry Measurement of Platinum and Gold Drugs in Cultured Lung Cancer Cells

In this study, we developed a strategy to determine atto- and femtomolar amounts of metal ions in lysates and mineralizates of cells (human non-small-cell lung carcinoma (NSCLC, A549) and normal lung (MRC-5)) exposed to cytotoxic metallo-drugs: cisplatin and auranofin at concentrations close to the half-maximal inhibitory drug concentrations (IC50). The developed strategy combines data obtained using biological and chemical approaches. Cell density was determined using two independent cell staining assays using trypan blue, calcein AM/propidium iodide. Metal concentrations in lysed and mineralized cells were established employing a mass spectrometer with inductively coupled plasma (ICP-MS) and equipped with a cross-flow nebulizer working in aspiration mode. It allowed for detecting of less than 1 fg of metal per cell. To decrease the required amount of sample material (from 1.5 mL to ~100 µL) without loss of sensitivity, the sample was introduced as a narrow band into a constant stream of liquid (flow-injection analysis). It was noticed that the selectivity of cisplatin accumulation by cells depends on the incubation time. This complex is accumulated by cells at a lower efficiency than auranofin and is found primarily in the lysate representing the cytosol. In contrast, auranofin interacts with water-insoluble compounds. Despite their different mechanism of action, both metallo-drugs increased the accumulation of transition metal ions responsible for oxidative stress.

Mismatch Repair Status in Patient-Derived Colorectal Cancer Organoids Does Not Affect Intrinsic Tumor Cell Sensitivity to Systemic Therapy

DNA mismatch repair deficiency (dMMR) in metastatic colorectal cancer (mCRC) is associated with poor survival and a poor response to systemic treatment. However, it is unclear whether dMMR results in a tumor cell-intrinsic state of treatment resistance, or whether alternative mechanisms play a role. To address this, we generated a cohort of MMR-proficient and -deficient Patient-Derived Organoids (PDOs) and tested their response to commonly used drugs in the treatment of mCRC, including 5-fluorouracil (5-FU), oxaliplatin, SN-38, binimetinib, encorafenib, and cetuximab. MMR status did not correlate with the response of PDOs to any of the drugs tested. In contrast, the presence of activating mutations in the KRAS and BRAF oncogenes was significantly associated with resistance to chemotherapy and sensitivity to drugs targeting oncogene-activated pathways. We conclude that mutant KRAS and BRAF impact the intrinsic sensitivity of tumor cells to chemotherapy and targeted therapy. By contrast, tumor cell-extrinsic mechanisms-for instance signals derived from the microenvironment-must underlie the association of MMR status with therapy response. Future drug screens on rationally chosen cohorts of PDOs have great potential in developing tailored therapies for specific CRC subtypes including, but not restricted to, those defined by BRAF/KRAS and MMR status.

Biological Activities of Extracts from Ageratum fastigiatum: Phytochemical Study and In Silico Target Fishing Approach

In the present study, the ethanolic extract from aerial parts of Ageratum fastigiatum was evaluated in vitro against epimastigote forms of Trypanosoma cruzi (Y strain), promastigote forms of Leishmania amazonensis (PH8 strain), and L. chagasi (BH400 strain). The extract was also evaluated against Staphylococcus aureus (ATCC 25 923), Escherichia coli (ATCC 11 775), Pseudomonas aeruginosa (ATCC 10 145), and Candida albicans (ATCC 36 802). The phytochemical screening was performed by thin-layer chromatography and high-performance liquid chromatography. The extract was fractionated using flash preparative chromatography. The ethanolic extract showed activity against T. cruzi, L. chagasi, and L. amazonensis and antimicrobial activity against S. aureus, E. coli, P. aeruginosa, and C. albicans. The phytochemical screening revealed coumarins, terpenes/sterols, and flavonoids in the ethanolic extract. In addition, the coumarin identified as ayapin was isolated from this extract. We also performed in silico prediction of potential biological activities and targets for compounds previously found in A. fastigiatum. Several predictions were confirmed both retrospectively and prospectively by experimental results described here or elsewhere. Some activities described in the in silico target fishing approach were validated by the ethnopharmacological use and known biological properties. Some new activities and/or targets were predicted and could guide future studies. These results suggest that A. fastigiatum can be an interesting source of substances with antiparasitic and antimicrobial activities.

Cotranslational prolyl hydroxylation is essential for flavivirus biogenesis

Viral pathogens are an ongoing threat to public health worldwide. Analysing their dependence on host biosynthetic pathways could lead to effective antiviral therapies1. Here we integrate proteomic analyses of polysomes with functional genomics and pharmacological interventions to define how enteroviruses and flaviviruses remodel host polysomes to synthesize viral proteins and disable host protein production. We find that infection with polio, dengue or Zika virus markedly modifies polysome composition, without major changes to core ribosome stoichiometry. These viruses use different strategies to evict a common set of translation initiation and RNA surveillance factors from polysomes while recruiting host machineries that are specifically required for viral biogenesis. Targeting these specialized viral polysomes could provide a new approach for antiviral interventions. For example, we find that both Zika and dengue use the collagen proline hydroxylation machinery to mediate cotranslational modification of conserved proline residues in the viral polyprotein. Genetic or pharmacological inhibition of proline hydroxylation impairs nascent viral polyprotein folding and induces its aggregation and degradation. Notably, such interventions prevent viral polysome remodelling and lower virus production. Our findings delineate the modular nature of polysome specialization at the virus-host interface and establish a powerful strategy to identify targets for selective antiviral interventions.

MuSyC is a consensus framework that unifies multi-drug synergy metrics for combinatorial drug discovery

Drug combination discovery depends on reliable synergy metrics but no consensus exists on the correct synergy criterion to characterize combined interactions. The fragmented state of the field confounds analysis, impedes reproducibility, and delays clinical translation of potential combination treatments. Here we present a mass-action based formalism to quantify synergy. With this formalism, we clarify the relationship between the dominant drug synergy principles, and present a mapping of commonly used frameworks onto a unified synergy landscape. From this, we show how biases emerge due to intrinsic assumptions which hinder their broad applicability and impact the interpretation of synergy in discovery efforts. Specifically, we describe how traditional metrics mask consequential synergistic interactions, and contain biases dependent on the Hill-slope and maximal effect of single-drugs. We show how these biases systematically impact synergy classification in large combination screens, potentially misleading discovery efforts. Thus the proposed formalism can provide a consistent, unbiased interpretation of drug synergy, and accelerate the translatability of synergy studies.

The lack of a unifying metric characterizing combinatorial drug interactions has impeded the development of combinatorial therapies. Here, the authors present MuSyC, a consensus synergy metric that overcomes several caveats associated with other, popular metrics.

A novel model-checking approach for dose-response relationships

We propose a test for assessing nonlinear dose-response models based on a Crámer-von Mises statistic. We establish the asymptotic distribution of the test and demonstrate that the test can detect the local alternative converging to the null at the parametric rate 1/n. We provide a bootstrap resampling technique to calculate the critical values. It is observed that the test has good power performance in small sample sizes. We apply the proposed method to analyze 250 datasets from a pharmacologic study and conduct two small simulation experiments to explore the numerical performance of the proposed test and compare one commonly used test in practice.

Super-Enhancer Redistribution as a Mechanism of Broad Gene Dysregulation in Repeatedly Drug-Treated Cancer Cells

Cisplatin is an antineoplastic drug administered at suboptimal and intermittent doses to avoid life-threatening effects. Although this regimen shortly improves symptoms in the short term, it also leads to more malignant disease in the long term. We describe a multilayered analysis ranging from chromatin to translation-integrating chromatin immunoprecipitation sequencing (ChIP-seq), global run-on sequencing (GRO-seq), RNA sequencing (RNA-seq), and ribosome profiling-to understand how cisplatin confers (pre)malignant features by using a well-established ovarian cancer model of cisplatin exposure. This approach allows us to segregate the human transcriptome into gene modules representing distinct regulatory principles and to characterize that the most cisplatin-disrupted modules are associated with underlying events of super-enhancer plasticity. These events arise when cancer cells initiate without ultimately ending the program of drug-stimulated death. Using a PageRank-based algorithm, we predict super-enhancer regulator ISL1 as a driver of this plasticity and validate this prediction by using CRISPR/dCas9-KRAB inhibition (CRISPRi) and CRISPR/dCas9-VP64 activation (CRISPRa) tools. Together, we propose that cisplatin reprograms cancer cells when inducing them to undergo near-to-death experiences.

Nonlinear responses of foliar phenylpropanoids to increasing O3 exposure: Ecological implications in a Populus model system

Plant phenolic compounds (phenylpropanoids) act as defense chemicals against herbivores and can mediate ecosystem processes. Tropospheric ozone (O₃) pollution alters concentrations of plant phenolics; however, little is known about how these phytochemicals respond to different levels of O₃ exposure. Here, we investigated the effects of five different O₃ exposure levels on foliar concentrations of phenylpropanoids (53 compounds in total) and antioxidative capacity in hybrid Populus (Populus euramericana cv. '74/76') saplings grown in the presence of high or low soil nitrogen (N) load. Increasing O₃ exposure initially increased and then decreased total concentrations of phenolic compounds, revealing a biphasic exposure-response profile (hormetic zone: 1.1-36.3 ppm h AOT40). This biphasic response pattern was driven by changes in a subset of phenylpropanoids with high antioxidative capacity (e.g. condensed tannins) but not in phenolics with low antioxidative capacity (e.g. salicinoids). The O₃ exposure-response relationships of some phenylpropanoids (e.g. flavonoids and chlorogenic acids) varied in response to soil N, with hormesis occurring in high N soil but not in low N soil. Collectively, our findings indicated that plant phenolic compounds exhibit nonlinear responses to increasing O₃ exposure, and that the responses vary in relation to phenolic compound class, antioxidative capacity, and soil nitrogen conditions. Our findings further suggest that the impact of O₃ on ecological processes mediated by phenolics will be concentration-dependent, highlighting the complexity of the ecological effects of ground-level O₃ pollution.

Luminescent cyclometalated platinum(ii) complexes with acyclic diaminocarbene ligands: structural, photophysical and biological properties

Four new cyclometalated Pt(ii) complexes bearing acyclic diaminocarbene (ADC) ligands, [Pt(C^N)Cl{C(NHXyl)(NHR)}] [C^N = 2,6-difluorophenylpyridine (dfppy), phenylquinoline (pq); R = Pr 3a, 4a, CH₂Ph 3b, 4b], were prepared by the nucleophilic attack on the isocyanide [Pt(C^N)Cl(CNXyl)] (C^N = dfppy 1, pq 2) by the corresponding amine RNH₂ (R = Pr, CH₂Ph). Complexes 3 show in their ¹H NMR spectra in CDCl₃ a notable concentration dependence, with a clear variation of the δ_H (NHXyl) signal, suggesting an assembling process implying donor-acceptor NH_XylCl bonding, also supported by 1D-PGSE (Pulse Field Gradient Spin Echo) and 2D-DOSY (Diffusion Ordered Spectroscopy) NMR experiments in solution and X-ray diffraction studies. The intermolecular interactions in compounds 3a and 3b were studied by using Hirshfeld surface analysis and Non-Covalent Interaction (NCI) methods on their X-ray structures. Their photophysical properties were investigated by absorption and emission spectroscopies and also by TD-DFT calculations performed on 3a and 4b. These complexes show green (3) or orange (4) phosphorescence, attributed to a mixed ³IL/³MLCT excited state. The carbene ligand does not affect the emission maxima but it produces an increase of the quantum yields in relation to the isocyanide in the precursors. In fluid solutions, the emission is not concentration-dependent, but the complexes may show aggregation induced emission as detailed for complexes 3a and 4a. In addition, cytotoxicity studies in the human cell lines A549 (lung carcinoma) and HeLa (cervix carcinoma) showed good activity for these complexes and 3a, 3b and 4a exhibit a strong effect on DNA electrophoretic mobility. To the best of our knowledge, compounds 3 and 4 represent the first examples of cycloplatinated complexes bearing acyclic diamino carbenes with antiproliferative properties.

A network meta-analysis of the dose-response effects of lurasidone on acute schizophrenia

We compared the efficacy, safety, and acceptability of lurasidone at different doses to establish the dose-response relationships of lurasidone therapeutic and adverse effects in acute schizophrenia. Included trials were 4- to 16-week, fixed-dose, randomized controlled trials of lurasidone in adults with acute schizophrenia. Different doses of lurasidone, other antipsychotics, and placebo were considered as independent treatments. Apart from all-cause dropout rates, four therapeutic and four adverse outcomes were included in the frequentist network meta-analysis (NMA). Lurasidone 160, 120, 80, 40, and 20 mg/day were studied in ten trials of 3,366 adults with schizophrenia exacerbation. Lurasidone 160 mg/day reduced Positive and Negative Syndrome Scale (PANSS) total scores significantly more than lurasidone 120, 80, 40, and 20 mg/day (mean differences = - 7.63, - 7.04, - 8.83, and - 12.25, respectively). All-cause dropout rates were significantly lower in participants receiving lurasidone 160 mg/day and 80 mg/day compared with those taking placebo. The half-maximal effective doses of lurasidone for PANSS total, PANSS positive, and MADRS score reductions were higher than 80 mg/day. The confidence of all NMA estimates was low or very low. Lurasidone 160 mg/day is currently the most efficacious and acceptable dose for acute schizophrenia. Its maximal effective doses may be higher than 160 mg/day.

Towards Quantitative and Standardized Serological and Neutralization Assays for COVID-19

Quantitative and robust serology assays are critical measurements underpinning global COVID-19 response to diagnostic, surveillance, and vaccine development. Here, we report a proof-of-concept approach for the development of quantitative, multiplexed flow cytometry-based serological and neutralization assays. The serology assays test the IgG and IgM against both the full-length spike antigens and the receptor binding domain (RBD) of the spike antigen. Benchmarking against an RBD-specific SARS-CoV IgG reference standard, the anti-SARS-CoV-2 RBD antibody titer was quantified in the range of 37.6 µg/mL to 31.0 ng/mL. The quantitative assays are highly specific with no correlative cross-reactivity with the spike proteins of MERS, SARS1, OC43 and HKU1 viruses. We further demonstrated good correlation between anti-RBD antibody titers and neutralizing antibody titers. The suite of serology and neutralization assays help to improve measurement confidence and are complementary and foundational for clinical and epidemiologic studies.