Therapeutic target discovery using Caenorhabditis elegans

Biochemometry identifies ostruthin as pluripotent antimicrobial and anthelmintic agent from masterwort

The root extract of Peucedanum ostruthium (PO-E) was identified as a promising antibacterial source from a screening of 158 extracts against Staphylococcus aureus. It has also recently been shown to significantly decrease the survival of the nematode Caenorhabditis elegans. We used the biochemometric approach ELINA to investigate the phytochemical characteristics of the multicomponent mixture PO-E to identify the anti-infective constituent(s) targeting S. aureus and C. elegans.1H NMR spectra of PO-E-derived microfractions were correlated with their respective bioactivity data. Heterocovariance analyses unambiguously identified ostruthin as an anti-staphylococcal constituent, which potently also inhibited Enterococcus spp.. ELINA demonstrated that anthelmintic activity was due to a combinatorial effect of ostruthin and isoimperatorin. A C. elegans-based survival and motility assay confirmed that isoimperatorin, imperatorin, and verapamil modulated the susceptibility of ostruthin. The combinatorial effect of these natural products was shown in larvae studies to be related to the function of the nematodes' efflux pump.

Caenorhabditis elegans as an In Vivo Model for the Discovery and Development of Natural Plant-Based Antimicrobial Compounds

Antimicrobial resistance (AMR) due to the prevalence of multidrug-resistant (MDR) pathogens is rapidly increasing worldwide, and the identification of new antimicrobial agents with innovative mechanisms of action is urgently required. Medicinal plants that have been utilised for centuries with minor side effects may hold great promise as sources of effective antimicrobial products. The free-living nematode Caenorhabditis elegans (C. elegans) is an excellent live infection model for the discovery and development of new antimicrobial compounds. However, while C. elegans has widely been utilised to explore the effectiveness and toxicity of synthetic antibiotics, it has not been used to a comparable extent for the analysis of natural products. By screening the PubMed database, we identified articles reporting the use of the C. elegans model for the identification of natural products endowed with antibacterial and antifungal potential, and we critically analysed their results. The studies discussed here provide important information regarding "in vivo" antimicrobial effectiveness and toxicity of natural products, as evaluated prior to testing in conventional vertebrate models, thereby supporting the relevance of C. elegans as a highly proficient model for their identification and functional assessment. However, their critical evaluation also underlines that the characterisation of active phytochemicals and of their chemical structure, and the unravelling of their mechanisms of action represent decisive challenges for future research in this area.

Mutant C. elegans p53 Together with Gain-of-Function GLP-1/Notch Decreases UVC-Damage-Induced Germline Cell Death but Increases PARP Inhibitor-Induced Germline Cell Death

The TP53 gene is mutated in over 50% of human cancers, and the C. elegansp53-1(cep-1) gene encodes the ortholog CEP-1. CEP-1 is activated by ultraviolet type C (UVC)-induced DNA damage and activates genes that induce germline apoptosis. UVC treatment of gain-of-function glp-1(ar202gf)/Notch tumorous animals reduces germline stem cell numbers (and overall tumor size), while UVC treatment of double-mutant cep-1/p53(gk138);glp-1/Notch(ar202gf) increases DNA damage adducts and stem cell tumor volume. We compared UVC-induced mitotic stem cell death and animal lifespans for the two different C. elegans tumorous strains. C. elegans stem cell compartment death has never been observed, and we used engulfed small stem cells, notable by green fluorescent puncta, to count cell death events. We found UVC treatment of glp-1(ar202gf) animals increased stem cell death and increased lifespan. However, UVC treatment of double-mutant cep-1/p53(gk138);glp-1/Notch(ar202gf) animals decreased stem cell death, increased tumor volume, and decreased animal lifespan. There are pharmacological agents that induce p53-independent cell death of human cells in culture; and two notable protocols are the PARP-trapping agents of temozolomide plus talazoparib and the nucleoside analogue 8-amino-adenosine. It is important to determine ways to rapidly test for pharmacological agents able to induce p53-independent cell death. We tested feeding cep-1/p53(gk138);glp-1/Notch(ar202gf) nematodes with either 8-amino-adenosine or temozolomide plus talazoparib and found both were able to decrease tumor volume. This is the first comparison for p53-independent responses in cep-1/p53(gk138);glp-1/Notch(ar202gf) animals and showed UVC DNA damage increased tumor volume and decreased lifespan while PARP inhibition decreased tumor volume.

From genes to drugs: target validation in Caenorhabditis elegans

A central challenge in post-genomic drug discovery is selection of relevant therapeutic targets from a large pool of candidates, so that resources are invested productively. Key to meeting this challenge is demonstrating target function in disease-related pathways in vivo. The nematode Caenorhabditis elegans, a well-characterized experimental system for genetic analysis of biological regulatory pathways, provides a powerful means of assessing the impact of modulating target function on biological processes, thus facilitating selection of high-value targets.:

Caenorhabditis elegans in regenerative medicine: a simple model for a complex discipline

Stem cell research is a major focus of regenerative medicine, which amalgamates diverse disciplines ranging from developmental cell biology to chemical and genetic therapy. Although embryonic stem cells have provided the foundation of stem cell therapy, they offer an in vitro study system that might not provide the best insight into mechanisms and behaviour of cells within living organisms. Caenorhabditis elegans is a well defined model organism with highly conserved cell development and signalling processes that specify cell fate. Its genetic amenability coupled with its chemical screening applicability make the nematode well suited as an in vivo system in which regenerative therapy and stem cell processes can be explored. Here, we describe some of the major advances in stem cell research from the worm's perspective.

Caenorhabditis elegans: modest increase of susceptibility to ivermectin in individual P-glycoprotein loss-of-function strains

P-glycoproteins (Pgps) are members of the ABC transporter superfamily and are involved in detoxification mechanisms of single- and multicellular organisms. Their importance for survival of organisms in the presence of harmful drug concentrations has been widely studied in cancer cells but Pgp-dependent drug resistance of parasites has also been demonstrated. Ivermectin (IVM), a widely used anthelmintic in human and veterinary medicine, is a known substrate at least of mammalian Pgps and resistance against IVM is proposed to be associated with Pgps. The consequences of loss of Pgp function for the development of the model nematode Caenorhabditis elegans were analysed in the presence of IVM. Either strains missing only a single Pgp were used or Pgp activity generally was inhibited using verapamil (VPL). Loss-of-function of individual Pgp resulted in a statistically significant increase in IVM susceptibility in terms of impaired development with decreases in EC₅₀ values between 1.5- and 4.3-fold. Absence of seven Pgps resulted in a higher impact on IVM susceptibility of C. elegans since it resulted in EC₅₀ values decreased by 2.4- to 4.3-fold. This increase in IVM susceptibility was even more pronounced than that observed when Pgp function was blocked in general by VPL (approximately 2.5-fold). This study demonstrates clearly that Pgps are of importance for IVM detoxification in the model organism C. elegans and that some Pgps obviously have a higher impact than others.

Simulative evaluation of taurine against alopecia caused by stress in Caenorhabditis elegans

Hair loss or alopecia has been portrayed as a modern malady which is aggravated by stressful conditions. Major cases of alopecia were found among individuals of 40s-50s, nowadays, even among the 20s-30s. This study characterized taurine's potential against alopecia caused by chemical stress agents based on the comparison with other commercially available anti-alopecia agents using Caenorhabditis elegans. The criteria used are their effects on the expression of stress markers and measurements of vital signs: lifespan comparison, progeny number, and mobility. C. elegans showed the typical stress symptoms under treatment with tunicamycin, endoplasmic reticulum stress agent. Hsp-70 protein expression increased, while worm's lifespan and per capita progeny number significantly decreased along with an unusually retarded movement. A positive response was shown when worms were treated with taurine along with astressin-B and finasteride. Between the treatments, finasteride showed better outcomes in terms of stress-reducing effects. Taurine helped worms recover more effectively from adverse influence of stress. In conclusion, there is strong evidence that taurine has a great potential as anti-alopecia effect especially against the one caused by the chemical stress. The present study implies that taurine might strongly work against hair loss when used in combination with other commercially available -anti-alopecia agents.

Contextual data integration in drug discovery

INTRODUCTION

The interpretation of high-throughput profiling data depends on the pathway analysis database. Currently, pathway analysis often has to rely on a set of interactions and pathways measured in every possible human tissue, due to insufficient knowledge about interactions and pathways in the context of the profiling experiment. However, a recent global scale analysis of human tissue proteomes and interactomes reveals significant differences among tissues, suggesting that interaction and pathway data that are used out of biological context are the major source of inaccuracies and noise in the analysis of profiling data.

AREAS COVERED

In this review, the major classes of biological context used for experimental detection of molecular interactions and pathways in molecular biology are described. Furthermore, the author reviews methods for predicting biological interactions in order to evaluate the applicability of various contextual interaction data in pathway analysis. Using the results from recent publications that study large-scale tissue composition, the article provides an estimation of the gain in pathway analysis accuracy if only the interactions predicted for the context of a molecular profiling experiment are used, relative to the analysis performed with a context-independent knowledge base.

EXPERT OPINION

It is of the author's opinion that the major source of inaccuracy in pathway analysis is the lack of knowledge about tissue-specific transcriptional regulation. It is therefore suggested that the accuracy of the analysis can be substantially improved if only context-specific interactions and pathways are used for interpretation.

Novel structural arrangement of nematode cystathionine β-synthases: characterization of Caenorhabditis elegans CBS-1

CBSs (cystathionine β-synthases) are eukaryotic PLP (pyridoxal 5 *-phosphate)-dependent proteins that maintain cellular homocysteine homoeostasis and produce cystathionine and hydrogen sulfide. In the present study, we describe a novel structural arrangement of the CBS enzyme encoded by the cbs-1 gene of the nematode Caenorhabditis elegans. The CBS-1 protein contains a unique tandem repeat of two evolutionarily conserved catalytic regions in a single polypeptide chain. These repeats include a catalytically active C-terminal module containing a PLP-binding site and a less conserved N-terminal module that is unable to bind the PLP cofactor and cannot catalyse CBS reactions, as demonstrated by analysis of truncated variants and active-site mutant proteins. In contrast with other metazoan enzymes, CBS-1 lacks the haem and regulatory Bateman domain essential for activation by AdoMet (S-adenosylmethionine) and only forms monomers. We determined the tissue and subcellular distribution of CBS-1 and showed that cbs-1 knockdown by RNA interference leads to delayed development and to an approximately 10-fold elevation of homocysteine concentrations in nematode extracts. The present study provides the first insight into the metabolism of sulfur amino acids and hydrogen sulfide in C. elegans and shows that nematode CBSs possess a structural feature that is unique among CBS proteins.

Stem cells: a model for screening, discovery and development of drugs

The identification of normal and cancerous stem cells and the recent advances made in isolation and culture of stem cells have rapidly gained attention in the field of drug discovery and regenerative medicine. The prospect of performing screens aimed at proliferation, directed differentiation, and toxicity and efficacy studies using stem cells offers a reliable platform for the drug discovery process. Advances made in the generation of induced pluripotent stem cells from normal or diseased tissue serves as a platform to perform drug screens aimed at developing cell-based therapies against conditions like Parkinson’s disease and diabetes. This review discusses the application of stem cells and cancer stem cells in drug screening and their role in complementing, reducing, and replacing animal testing. In addition to this, target identification and major advances in the field of personalized medicine using induced pluripotent cells are also discussed.

The nematode C. elegans as an animal model to explore toxicology in vivo: solid and axenic growth culture conditions and compound exposure parameters

Significant limitations in vertebrate animal model systems include the time involved, the expense, the fact that in vitro results may not reflect live animal pathology, difficulties in transporting the toxin past the blood brain barrier, and the inability to identify the mechanism of action without some a priori knowledge of the toxin's target. The availability of the complete genome sequence of the nematode C. elegans, coupled with the worm's size, growth rate, ease of culturing, and the realization that basic biological mechanisms and disease processes between worms and humans are highly conserved, makes this genetically tractable model a remarkable opportunity to dissect and identify in vivo the cellular processes involved in toxin-induced cell dysregulation and death. This unit includes protocols for culturing worms on solid and axenic media and acute and chronic exposure parameters for Parkinson's disease-associated toxins and hemin chloride. These methods provide the groundwork for using this powerful model system to further elucidate and understand the molecular mechanisms involved in nutrition as well as toxicological responses relevant to human diseases.

Taurine reduces ER stress in C. elegans

Background

ER stress is a strong indicator of whether or not a cell is undergoing physiological stress. C. elegans is a practical system of characterizing the effect of ER stress at the in vivo or organismal level.

Methods

This study characterized taurine’s anti-ER stress potential employing western blotting on ER stress markers and assays of motility, lifespan comparison, and fecundity measurement.

Results

When treated with tunicamycin, C. elegans showed the typical ER stress symptoms. It showed a higher expression of hsp-70 and skn-1 than the non-treated control. Survivorship significantly decreased under tunicamycin treatment, and the offspring number also decreased. During the synchronized culture under ER stress conditions, the C. elegans showed early signs of aging especially between L3 and L4 within their life span, along with lowered motility. The worms, however, showed a positive response to the taurine treatment under ER stress conditions.

Conclusions

When C. elegans were treated with taurine before or after the tunicamycin treatment, they showed a less severe level of ER stress, including an enhanced survivorship, increased motility, and augmented fecundity. Taken together, these results strongly indicate that taurine works positively to cope with ER stress from the organismal perspective.

Multi-environment model estimation for motility analysis of Caenorhabditis elegans

The nematode Caenorhabditis elegans is a well-known model organism used to investigate fundamental questions in biology. Motility assays of this small roundworm are designed to study the relationships between genes and behavior. Commonly, motility analysis is used to classify nematode movements and characterize them quantitatively. Over the past years, C. elegans' motility has been studied across a wide range of environments, including crawling on substrates, swimming in fluids, and locomoting through microfluidic substrates. However, each environment often requires customized image processing tools relying on heuristic parameter tuning. In the present study, we propose a novel Multi-Environment Model Estimation (MEME) framework for automated image segmentation that is versatile across various environments. The MEME platform is constructed around the concept of Mixture of Gaussian (MOG) models, where statistical models for both the background environment and the nematode appearance are explicitly learned and used to accurately segment a target nematode. Our method is designed to simplify the burden often imposed on users; here, only a single image which includes a nematode in its environment must be provided for model learning. In addition, our platform enables the extraction of nematode ‘skeletons’ for straightforward motility quantification. We test our algorithm on various locomotive environments and compare performances with an intensity-based thresholding method. Overall, MEME outperforms the threshold-based approach for the overwhelming majority of cases examined. Ultimately, MEME provides researchers with an attractive platform for C. elegans' segmentation and ‘skeletonizing’ across a wide range of motility assays.

Use of non-mammalian alternative models for neurotoxicological study

The field of neurotoxicology needs to satisfy two opposing demands: the testing of a growing list of chemicals, and resource limitations and ethical concerns associated with testing using traditional mammalian species. National and international government agencies have defined a need to reduce, refine or replace mammalian species in toxicological testing with alternative testing methods and non-mammalian models. Toxicological assays using alternative animal models may relieve some of this pressure by allowing testing of more compounds while reducing expense and using fewer mammals. Recent advances in genetic technologies and the strong conservation between human and non-mammalian genomes allow for the dissection of the molecular pathways involved in neurotoxicological responses and neurological diseases using genetically tractable organisms. In this review, applications of four non-mammalian species, zebrafish, cockroach, Drosophila, and Caenorhabditis elegans, in the investigation of neurotoxicology and neurological diseases are presented.

High-throughput screening of small molecules for bioactivity and target identification in Caenorhabditis elegans

This protocol describes a procedure for screening small molecules for bioactivity and a genetic approach to target identification using the nematode Caenorhabditis elegans as a model system. Libraries of small molecules are screened in 24-well plates that contain a solid agar substrate. On top of the agar mixture, one small-molecule species is deposited into each well, along with worm food (E. coli), and two third-stage or fourth-stage larval worms using a COPAS (Complex Object Parametric Analyzer and Sorter) Biosort. Three to five days later the plates are screened for phenotype. Images of the wells are acquired and archived using a HiDI 2100 automated imaging system (Elegenics). Up to 2,400 chemicals can be screened per week. To identify the predicted protein target of a bioactive molecule, wild-type worms are mutagenized using ethylmethanesulfonate (EMS). Progeny are screened for individuals resistant to the molecules effects. The candidate mutant target that confers resistance is then identified. Target identification might take months.

Nematodes, bacteria, and flies: a tripartite model for nematode parasitism

More than a quarter of the world's population is infected with nematode parasites, and more than a hundred species of nematodes are parasites of humans [1-3]. Despite extensive morbidity and mortality caused by nematode parasites, the biological mechanisms of host-parasite interactions are poorly understood, largely because of the lack of genetically tractable model systems. We have demonstrated that the insect parasitic nematode Heterorhabditis bacteriophora, its bacterial symbiont Photorhabdus luminescens, and the fruit fly Drosophila melanogaster constitute a tripartite model for nematode parasitism and parasitic infection. We find that infective juveniles (IJs) of Heterorhabditis, which contain Photorhabdus in their gut, can infect and kill Drosophila larvae. We show that infection activates an immune response in Drosophila that results in the temporally dynamic expression of a subset of antimicrobial peptide (AMP) genes, and that this immune response is induced specifically by Photorhabdus. We also investigated the cellular and molecular mechanisms underlying IJ recovery, the developmental process that occurs in parasitic nematodes upon host invasion and that is necessary for successful parasitism. We find that the chemosensory neurons and signaling pathways that control dauer recovery in Caenorhabditis elegans also control IJ recovery in Heterorhabditis, suggesting conservation of these developmental processes across free-living and parasitic nematodes.

Early onset of regionalization in EMS lineage of C. elegans embryo: a quantitative study

Early localization of C. elegans founder cell descendents in certain regions of embryo has been documented. The purpose of this investigation is to evaluate the onset of ABp and EMS descendent cell regionalization in the embryo using the random motility coefficient as a quantitative parameter. The forward migration index (FMI) was also calculated in order to evaluate the chemotatic biases of ABp-dc and EMS-dc during regionalization. The results showed that the random motility coefficient declined as the cells tended to regionalize. The mean squared displacement (MSD) versus time plot showed a non-linear model which indicated non-random cell movement. FMI showed progressive increase as the cells tended to regionalized, and it was significantly higher in EMS-dc than ABp-dc, moreover the chemotatic biases were higher in EMS-dc than ABp-dc. The circular plots showed that the statistical differences between the two lineages were significant, while ABp-dc showed significant differences in xy, xz and yz planes; EMS derived cells showed no significant differences except in yz planes. The conclusion of this study is that the onset of early regionalization occurs in EMS-dc sooner than in ABp-dc.

The Caenorhabditis elegans dopaminergic system: opportunities for insights into dopamine transport and neurodegeneration

The neurotransmitter dopamine (DA) plays a central role in the coordination of movement, attention, and the recognition of reward. Loss of DA from the basal ganglia, as a consequence of degeneration of neurons in the substantia nigra, triggers postural instability and Parkinson's disease (PD). DA transporters (DATs) regulate synaptic DA availability and provide a conduit for the uptake of DA mimetic neurotoxins, which can be used to evoke neuronal death and Parkinson-like syndrome. Recently, we have explored the sensitivity of DA neurons in the nematode Caenorhabditis elegans to the Parkinsonian-inducing neurotoxin 6-hydroxydopamine (6-OHDA) and found striking similarities, including DAT dependence, to neurodegeneration observed in mammalian models. In this review, we present our findings in the context of molecular and behavioral dimensions of DA signaling in C. elegans with an eye toward opportunities for uncovering DAT mutants, DAT regulators, and components of toxin-mediated cell death.

Comparing nuclear receptors in worms, flies and humans

Complete nucleotide sequences are now available for different species of the animal kingdom: Caenorhabditis elegans - a nematode, Drosophila - an insect, and humans - a mammal. Such information makes it possible to compare the set of nuclear receptors found in these organisms, and to discuss the possible reasons for the differences observed. The human genome sequencing identified few new receptors, which implies that most nuclear receptors have now been found. However, information about polymorphisms and regulating sequences, obtained through genomic sequencing, will be important for understanding receptor function and disease mechanisms. The surprisingly large number of nuclear receptors in C. elegans might have implications for the development of pharmaceuticals and the understanding of the function of these animals. By contrast, Drosophila has few nuclear receptors; however, examination of the unique nuclear receptors provides information about the function of these receptors.

Taking a functional genomics approach in molecular medicine

The elucidation of genetic components of human diseases at the molecular level provides crucial information for developing future causal therapeutic intervention. High-throughput genome sequencing and systematic experimental approaches are fuelling strategic programs designed to investigate gene function at the biochemical, cellular and organism levels. Bioinformatics is one important tool in functional genomics, although showing clear limitations in predicting ab initio gene structures, gene function and protein folds from raw sequence data. Systematic large-scale data-set generation, using the same type of experiments that are used to decipher the function of single genes, are being applied on entire genomes. Comparative genomics, establishment of gene catalogues, and investigation of cellular and tissue molecular profiles are providing essential tools for understanding gene function in complex biological networks.

From symptomatic treatments to causative therapy?

The search for genes that predispose individuals to develop common chronic diseases such as asthma, diabetes and Alzheimer's promises to give insights into their molecular pathogenesis. This will lead to the development of therapies that modulate the pathology, rather than the physiology of these diseases. As academia and the pharmaceutical industry increasingly focus on this challenge, the genetic dissection of Alzheimer's is spearheading attempts to shift the therapeutic paradigm away from symptomatic to curative treatments.