A Novel Cellular Spheroid-Based Autophagy Screen Applying Live Fluorescence Microscopy Identifies Nonactin as a Strong Inducer of Autophagosomal Turnover

Unraveling rosmarinic acid anticancer mechanisms in oral cancer malignant transformation

Oral squamous cell carcinoma (OSCC) is expected to rise ca. 40 % by 2040. Rosmarinic acid (RA) has been recognized for its anticancer properties, although its role in OSCC has been neglected. This work exploits the activity of RA in 2D and 3D models of OSCC cells to compel a roadmap for its anticancer properties. The results demonstrated that RA significantly reduced cell mass and metabolic activity in a dose, time, and cell-type-dependent manner, predominantly in highly-invasive OSCC, without compromising normal mucosa in therapeutic doses. RA decreased mitochondria membrane potential and increased redox state, which was corroborated by pioneering observations on the metabolome landscape of OSCC cells (glutathione reduction and acetate and fumarate release). RA triggered autophagy, upregulating BNIP3 and BCNL1 and downregulating BIRC5. The upregulation of CADM1 and downregulation of VIM, CADM2, SNAIL1, and SOX9 highlighted the modulation of epithelial-mesenchymal transition and the remodeling of the extracellular matrix by the downregulation of MMP-2 and MMP-9. RA interacts with P-glycoprotein with the highest docking score of -6.4 kcal/mol. The HSC-3 cell surface charge decreased after RA treatment (-22.6 ± 0.3 mV vs. -26.3 ± 0.3 mV, p < 0.0001), suggesting a reversion of cell polarity and the impairment of invasion. RA also shrank the growth and the metabolic activity of multicellular tumor spheroids. Its modest protein binding with human saliva sheds light on its administration by the oromucosal route. Overall, this work supports the need for further research on the anticancer potential of RA in OSCC, either in monotherapy, combined with conventional treatments, or conveyed in nanosystems.

Artificial intelligence and machine learning in clinical pharmacological research

BACKGROUND

Clinical pharmacology research has always involved computational analysis. With the abundance of drug-related data available, the integration of artificial intelligence (AI) and machine learning (ML) methods has emerged as a promising way to enhance clinical pharmacology research.

METHODS

Based on an accepted definition of clinical pharmacology as a field of research dealing with all aspects of drug-human interactions, the analysis included publications from institutes specializing in clinical pharmacology. Research topics and the most used machine learning methods in clinical pharmacology were retrieved from the PubMed database and summarized.

RESULTS

ML was identified in 674 publications attributed to clinical pharmacology research, with a significant increase in publication activity over the last decade. Notable research topics addressed by ML/AI included Covid-19-related clinical pharmacology research, clinical neuropharmacology, drug safety and risk assessment, clinical pharmacology related to cancer research, and antimicrobial and antiviral research unrelated to Covid-19. In terms of ML methods, neural networks, random forests, and support vector machines were frequently mentioned in the abstracts of the retrieved papers.

CONCLUSIONS

ML, and AI in general, is increasingly being used in various research areas within clinical pharmacology. This report presents specific examples of applications and highlights the most used ML methods.

Marine-Derived Natural Product HDYL-GQQ-495 Targets P62 to Inhibit Autophagy

Autophagy is widely implicated in pathophysiological processes such as tumors and metabolic and neurodegenerative disorders, making it an attractive target for drug discovery. Several chemical screening approaches have been developed to uncover autophagy-modulating compounds. However, the modulation capacity of marine compounds with significant pharmacological activities is largely unknown. We constructed an EGFP^KI-LC3B cell line using the CRISPR/Cas9 knock-in strategy in which green fluorescence indicated endogenous autophagy regulation. Using this cell line, we screened a compound library of approximately 500 marine natural products and analogues to investigate molecules that altered the EGFP fluorescence. We identified eight potential candidates that enhanced EGFP fluorescence, and HDYL-GQQ-495 was the leading one. Further validation with immunoblotting demonstrated that cleaved LC3 was increased in dose- and time-dependent manners, and the autophagy adaptor P62 showed oligomerization after HDYL-GQQ-495 treatment. We also demonstrated that HDYL-GQQ-495 treatment caused autophagy substrate aggregation, which indicated that HDYL-GQQ-495 serves as an autophagy inhibitor. Furthermore, HDYL-GQQ-495 induced Gasdermin E (GSDME) cleavage and promoted pyroptosis. Moreover, HDYL-GQQ-495 directly combined with P62 to induce P62 polymerization. In P62 knockout cells, the cleavage of LC3 or GSDME was blocked after HDYL-GQQ-495 treatment. The EGFP^KI-LC3B cell line was an effective tool for autophagy modulator screening. Using this tool, we found a novel marine-derived compound, HDYL-GQQ-495, targeting P62 to inhibit autophagy and promote pyroptosis.

Natural products targeting cancer cell dependency

Precision cancer medicine is a tailored treatment approach for individual cancer patients with different genomic characteristics. Mutated or hyperactive oncogenes have served as main drug targets in current precision cancer medicine, while defective or inactivated tumor suppressors in general have not been considered as druggable targets. Synthetic lethality is one of very few approaches that enable to target defective tumor suppressors with pharmacological agents. Synthetic lethality exploits cancer cell dependency on a protein or pathway, which arises when the function of a tumor suppressor is defective. This approach has been proven to be effective in clinical settings since the successful clinical introduction of BRCA-PARP synthetic lethality for the treatment of breast and ovarian cancer with defective BRCA. Subsequently, large-scale screenings with RNAi, CRISPR/Cas9-sgRNAs, and chemical libraries have been applied to identify synthetic lethal partners of tumor suppressors. Natural products are an important source for the discovery of pharmacologically active small molecules. However, little effort has been made in the discovery of synthetic lethal small molecules from natural products. This review introduces recent advances in the discovery of natural products targeting cancer cell dependency and discusses potentials of natural products in the precision cancer medicine.

Activated CAMKKβ-AMPK signaling promotes autophagy in a spheroid model of ovarian tumour metastasis

Background

A hallmark of epithelial ovarian cancer (EOC) metastasis is the process of spheroid formation, whereby tumour cells aggregate into 3D structures while in suspension in the peritoneal cavity. EOC spheroids are subjected to bioenergetic stress, thereby activating AMP-activated protein kinase (AMPK) signaling to enter a metabolically quiescent state, which can facilitate cell survival under nutrient-limiting conditions. Independently, we have also demonstrated that EOC spheroids induce autophagy, a process that degrades and recycles intracellular components to restore energy and metabolites. Herein, we sought to examine whether AMPK controls autophagy induction as a cell survival mechanism in EOC spheroids.

Results

We observed a co-ordinate increase in phosphorylated AMPK and the autophagy marker LC3-II during EOC spheroid formation. Reduced AMPK expression by siRNA-mediated knockdown of PRKAA1 and PRKAA2 blocked autophagic flux in EOC spheroids as visualized by fluorescence microscopy using the mCherry-eGFP-LC3B reporter. A complementary approach using pharmacologic agents Compound C and CAMKKβ inhibitor STO-609 to inhibit AMPK activity both yielded a potent blockade of autophagic flux as well. However, direct activation of AMPK in EOC cells using oligomycin and metformin was insufficient to induce autophagy. STO-609 treatment of EOC spheroids resulted in reduced viability in 7 out of 9 cell lines, but with no observed effect in non-malignant FT190 cell spheroids.

Conclusions

Our results support the premise that CAMKKβ-mediated AMPK activity is required, at least in part, to regulate autophagy induction in EOC spheroids and support cell viability in this in vitro model of EOC metastasis.

On the relevance of precision autophagy flux control in vivo - Points of departure for clinical translation

Macroautophagy (which we will call autophagy hereafter) is a critical intracellular bulk degradation system that is active at basal rates in eukaryotic cells. This process is embedded in the homeostasis of nutrient availability and cellular metabolic demands, degrading primarily long-lived proteins and specific organelles.. Autophagy is perturbed in many pathologies, and its manipulation to enhance or inhibit this pathway therapeutically has received considerable attention. Although better probes are being developed for a more precise readout of autophagic activity in vitro and increasingly in vivo, many questions remain. These center in particular around the accurate measurement of autophagic flux and its translation from the in vitro to the in vivo environment as well as its clinical application. In this review, we highlight key aspects that appear to contribute to stumbling blocks on the road toward clinical translation and discuss points of departure for reaching some of the desired goals. We discuss techniques that are well aligned with achieving desirable spatiotemporal resolution to gather data on autophagic flux in a multi-scale fashion, to better apply the existing tools that are based on single-cell analysis and to use them in the living organism. We assess how current techniques may be used for the establishment of autophagic flux standards or reference points and consider strategies for a conceptual approach on titrating autophagy inducers based on their effect on autophagic flux . Finally, we discuss potential solutions for inherent controls for autophagy analysis, so as to better discern systemic and tissue-specific autophagic flux in future clinical applications.Abbreviations: GFP: Green fluorescent protein; J: Flux; MAP1LC3/LC3: Microtubule-associated protein 1 light chain 3; nA: Number of autophagosomes; TEM: Transmission electron microscopy; τ: Transition time.

Chemical Screening Approaches Enabling Drug Discovery of Autophagy Modulators for Biomedical Applications in Human Diseases

Autophagy is an intracellular degradation pathway for malfunctioning aggregation-prone proteins, damaged organelles, unwanted macromolecules and invading pathogens. This process is essential for maintaining cellular and tissue homeostasis that contribute to organismal survival. Autophagy dysfunction has been implicated in the pathogenesis of diverse human diseases, and therefore, therapeutic exploitation of autophagy is of potential biomedical relevance. A number of chemical screening approaches have been established for the drug discovery of autophagy modulators based on the perturbations of autophagy reporters or the clearance of autophagy substrates. These readouts can be detected by fluorescence and high-content microscopy, flow cytometry, microplate reader and immunoblotting, and the assays have evolved to enable high-throughput screening and measurement of autophagic flux. Several pharmacological modulators of autophagy have been identified that act either via the classical mechanistic target of rapamycin (mTOR) pathway or independently of mTOR. Many of these autophagy modulators have been demonstrated to exert beneficial effects in transgenic models of neurodegenerative disorders, cancer, infectious diseases, liver diseases, myopathies as well as in lifespan extension. This review describes the commonly used chemical screening approaches in mammalian cells and the key autophagy modulators identified through these methods, and highlights the therapeutic benefits of these compounds in specific disease contexts.

In Vitro Screening Platforms for Identifying Autophagy Modulators in Mammalian Cells

Autophagy is a vital homeostatic pathway essential for cellular survival and human health. It primarily functions as an intracellular degradation process for the turnover of aggregation-prone proteins and unwanted organelles. Dysregulation of autophagy underlying diverse human diseases reduces cell viability, whereas stimulation of autophagy is cytoprotective in a number of transgenic disease models including neurodegenerative disorders. Thus, therapeutic exploitation of autophagy is considered a potential treatment strategy in certain human diseases, and therefore, chemical inducers of autophagy have tremendous biomedical relevance. In this review, we describe the in vitro screening platforms to identify autophagy modulators in mammalian cells using various methodologies including fluorescence and high-content imaging, flow cytometry, fluorescence and luminescence detection by microplate reader, immunoblotting, and immunofluorescence. The commonly used autophagy reporters in these screening platforms are either based on autophagy marker like LC3 or autophagy substrate such as aggregation-prone proteins or p62/SQSTM1. The reporters and assays for monitoring autophagy are evolving over time to become more sensitive in measuring autophagic flux with the capability of high-throughput applications for drug discovery. Here we highlight these developments and also describe the stringent secondary autophagy assays for characterizing the autophagy modulators arising from the primary screen. Since autophagy is implicated in myriad human physiological and pathological conditions, these technologies will enable identifying novel chemical modulators or genetic regulators of autophagy that will be of biomedical and fundamental importance to human health.

Modulation of quantum dots and clearance of Helicobacter pylori with synergy of cell autophagy

Helicobacter pylori (Hp) is one type of Gram-negative pathogenic bacterium that colonizes and causes a wide range of gastric diseases. Once Hp penetrates into cells, the currently recognized triple or quadruple therapy often loses effectiveness. Recent evidence suggests that autophagy is closely associated with Hp infection, and can play an important role in the eradication of Hp. More importantly, certain types of quantum dots (QDs) can induce and modulate cellular autophagy, and can be developed into conjugates making QDs potential candidates as new anti-Hp agents.