Drug screens of NGLY1 Deficiency worm and fly models reveal catecholamine, NRF2 and anti-inflammatory pathway activation as clinical approaches

AbstractN-glycanase 1/NGLY1 Deficiency is an ultra-rare and complex monogenic glycosylation disorder that affects fewer than 40 patients globally. NGLY1 Deficiency has been studied in model organisms such as yeast, worms, flies and mice. Proteasomal and mitochondrial homeostasis gene networks are controlled by the evolutionarily conserved transcriptional regulator Nrf1, whose activity requires deglycosylation by NGLY1. Hypersensitivity to the proteasome inhibitor bortezomib is a common phenotype observed in whole animal and cellular models of NGLY1 Deficiency. Here we describe unbiased phenotypic drug screens to identify FDA approved drugs, generally recognized as safe natural products and novel chemical entities that rescue growth and development of NGLY1-deficient worm and fly larvae treated with a toxic dose of bortezomib. We used image-based larval size and number assays for use in screens of a 2,560-member drug repurposing library and a 20,240-member lead discovery library. A total of 91 validated hit compounds from primary invertebrate screens were tested in a human cell line in a NRF2 activity assay. NRF2 is a transcriptional regulator that regulates cellular redox homeostasis and it can compensate for loss of Nrf1. Plant-based polyphenols comprise the largest class of hit compounds and NRF2 inducers. Catecholamines and catecholamine receptor activators comprise the second largest class of hits. Steroidal and non-steroidal anti-inflammatory drugs comprise the third largest class. Only one compound was active in all assays and species: the atypical antipsychotic and dopamine receptor agonist aripiprazole. Worm and fly models of NGLY1 Deficiency validate therapeutic rationales for activation of NRF2 and anti-inflammatory pathways based on results in mice and human cell models and suggest a novel therapeutic rationale for boosting catecholamine levels and/or signaling in the brain.

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The metabolite GLP‐1 (9‐36) is neuroprotective and anti‐inflammatory in cellular models of neurodegeneration

Journal of Neurochemistry ◽

10.1111/jnc.15521 ◽

2021 ◽

Author(s):

Yazhou Li ◽

Elliot J. Glotfelty ◽

Tobias Karlsson ◽

Lowella V. Fortuno ◽

Brandon K. Harvey ◽

...

Keyword(s):

Cellular Models ◽

Anti Inflammatory

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Exosome and Melatonin Additively Attenuates Inflammation by Transferring miR-34a, miR-124, and miR-135b

BioMed Research International ◽

10.1155/2020/1621394 ◽

2020 ◽

Vol 2020 ◽

pp. 1-9

Author(s):

June Seok Heo ◽

Ja-Yun Lim ◽

Dae Wui Yoon ◽

Sangshin Pyo ◽

Jinkwan Kim

Keyword(s):

Ex Vivo ◽

Inflammatory Diseases ◽

Underlying Mechanism ◽

M2 Macrophages ◽

Necrosis Factor Alpha ◽

Cellular Models ◽

Positive Effects ◽

Cell Based Therapy ◽

Anti Inflammatory ◽

Inflammatory Modulation

The positive effects of mesenchymal stem cells (MSCs) are primarily activated through molecular secretions known as paracrine activity, which regulates the function of various cell types including immune cells. Accumulating evidence shows that exosomes of soluble factors released from MSCs are potential alternative agents for stem cell-based therapy, although the exact underlying mechanism has not been elucidated. The purpose of this study was to evaluate the potential effects of exosomes produced by adipose-derived MSCs and to examine the changes in anti-inflammatory genes in concurrence with the polarization of M2 macrophages in cellular models ex vivo. Isolated exosomes were used to investigate the inflammatory modulation in pro-inflammatory cytokine-treated fibroblasts and THP-1 cells. The anti-inflammatory mRNA expression associated with M2 macrophages was significantly upregulated after exosome treatment in an interferon gamma and tumor necrosis factor alpha-treated inflammatory environment. Furthermore, melatonin-stimulated exosomes exerted superior anti-inflammatory modulation via exosomal miRNAs miR-34a, miR-124, and miR-135b, compared with exosomes. Our results indicate that melatonin-stimulated exosomes originating from adipose-derived MSCs are safe and efficient tools for regenerative medicine to treat inflammatory diseases.

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Recommended Guidelines for Developing, Qualifying, and Implementing Complex In Vitro Models (CIVMs) for Drug Discovery

SLAS DISCOVERY Advancing Life Sciences ◽

10.1177/2472555220923332 ◽

2020 ◽

Vol 25 (10) ◽

pp. 1174-1190

Author(s):

Jason E. Ekert ◽

Julianna Deakyne ◽

Philippa Pribul-Allen ◽

Rebecca Terry ◽

Christopher Schofield ◽

...

Keyword(s):

Drug Discovery ◽

Early Stage ◽

Cell Types ◽

In Vitro Models ◽

Success Rates ◽

Lead Discovery ◽

Cellular Models ◽

Discovery Phase ◽

Early Drug

The pharmaceutical industry is continuing to face high research and development (R&D) costs and low overall success rates of clinical compounds during drug development. There is an increasing demand for development and validation of healthy or disease-relevant and physiological human cellular models that can be implemented in early-stage discovery, thereby shifting attrition of future therapeutics to a point in discovery at which the costs are significantly lower. There needs to be a paradigm shift in the early drug discovery phase (which is lengthy and costly), away from simplistic cellular models that show an inability to effectively and efficiently reproduce healthy or human disease-relevant states to steer target and compound selection for safety, pharmacology, and efficacy questions. This perspective article covers the various stages of early drug discovery from target identification (ID) and validation to the hit/lead discovery phase, lead optimization, and preclinical safety. We outline key aspects that should be considered when developing, qualifying, and implementing complex in vitro models (CIVMs) during these phases, because criteria such as cell types (e.g., cell lines, primary cells, stem cells, and tissue), platform (e.g., spheroids, scaffolds or hydrogels, organoids, microphysiological systems, and bioprinting), throughput, automation, and single and multiplexing endpoints will vary. The article emphasizes the need to adequately qualify these CIVMs such that they are suitable for various applications (e.g., context of use) of drug discovery and translational research. The article ends looking to the future, in which there is an increase in combining computational modeling, artificial intelligence and machine learning (AI/ML), and CIVMs.

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Transcriptome Analysis in Domesticated Species: Challenges and Strategies

Bioinformatics and Biology Insights ◽

10.4137/bbi.s29334 ◽

2015 ◽

Vol 9S4 ◽

pp. BBI.S29334 ◽

Cited By ~ 4

Author(s):

Jessica P. Hekman ◽

Jennifer L Johnson ◽

Anna V. Kukekova

Keyword(s):

Complex Traits ◽

Gene Networks ◽

Association Studies ◽

Cultural Value ◽

Genomic Research ◽

Model Organisms ◽

Genome Wide Association Studies ◽

Rna Seq ◽

Genome Wide ◽

Genome Assemblies

Domesticated species occupy a special place in the human world due to their economic and cultural value. In the era of genomic research, domesticated species provide unique advantages for investigation of diseases and complex phenotypes. RNA sequencing, or RNA-seq, has recently emerged as a new approach for studying transcriptional activity of the whole genome, changing the focus from individual genes to gene networks. RNA-seq analysis in domesticated species may complement genome-wide association studies of complex traits with economic importance or direct relevance to biomedical research. However, RNA-seq studies are more challenging in domesticated species than in model organisms. These challenges are at least in part associated with the lack of quality genome assemblies for some domesticated species and the absence of genome assemblies for others. In this review, we discuss strategies for analyzing RNA-seq data, focusing particularly on questions and examples relevant to domesticated species.

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Identifying essential genes across eukaryotes by machine learning

10.1101/2021.04.15.439934 ◽

2021 ◽

Author(s):

Thomas Beder ◽

Olufemi Aromolaran ◽

Juergen Doenitz ◽

Sofia Tapanelli ◽

Eunice Oluwatobiloba Adedeji ◽

...

Keyword(s):

Machine Learning ◽

Cell Line ◽

Human Cell ◽

Population Studies ◽

Single Cells ◽

Human Cell Line ◽

Essential Genes ◽

Model Organisms ◽

A Genome ◽

Conserved Genes

Identifying essential genes on a genome scale is resource intensive and has been performed for only a few eukaryotes. For less studied organisms essentiality might be predicted by gene homology. However, this approach cannot be applied to non-conserved genes. Additionally, divergent essentiality information is obtained from studying single cells or whole, multi-cellular organisms, and particularly when derived from human cell line screens and human population studies. We employed machine learning across six model eukaryotes and 60,381 genes, using 41,635 features derived from sequence, gene functions and network topology. Within a leave-one-organism-out cross-validation, the classifiers showed a high generalizability with an average accuracy close to 80% in the left-out species. As a case study, we applied the method to Tribolium castaneum and validated predictions experimentally yielding similar performance. Finally, using the classifier based on the studied model organisms enabled linking the essentiality information of human cell line screens and population studies.

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Diverse biological processes coordinate the transcriptional response to nutritional changes in a Drosophila melanogaster multiparent population

10.1101/712984 ◽

2019 ◽

Author(s):

E. Ng’oma ◽

P.A. Williams-Simon ◽

A. Rahman ◽

E.G. King

Keyword(s):

Gene Expression ◽

Gene Networks ◽

Sequence Data ◽

Nutrient Sensing ◽

Gene Set Enrichment Analysis ◽

Tissue Type ◽

Model Organisms ◽

Laboratory Model ◽

Fisher Exact Test ◽

Tissue Samples

AbstractBackgroundEnvironmental variation in the amount of resources available to populations challenge individuals to optimize the allocation of those resources to key fitness functions. This coordination of resource allocation relative to resource availability is commonly attributed to key nutrient sensing gene pathways in laboratory model organisms, chiefly the insulin/TOR signaling pathway. However, the genetic basis of diet-induced variation in gene expression is less clear.ResultsTo describe the natural genetic variation underlying nutrient-dependent differences, we used an outbred panel derived from a multiparental population, the Drosophila Synthetic Population Resource. We analyzed RNA sequence data from multiple female tissue samples dissected from flies reared in three nutritional conditions: high sugar (HS), dietary restriction (DR), and control (C) diets. A large proportion of genes in the experiment (19.6% or 2,471 genes) were significantly differentially expressed for the effect of diet, 7.8% (978 genes) for the effect of the interaction between diet and tissue type (LRT, Padj. < 0.05). Interestingly, we observed similar patterns of gene expression relative to the C diet, in the DR and HS treated flies, a response likely reflecting diet component ratios. Hierarchical clustering identified 21 robust gene modules showing intra-modularly similar patterns of expression across diets, all of which were highly significant for diet or diet-tissue interaction effects (false discovery rate, FDR Padj. < 0.05). Gene set enrichment analysis for different diet-tissue combinations revealed a diverse set of pathways and gene ontology (GO) terms (two-sample t-test, FDR < 0.05). GO analysis on individual co-expressed modules likewise showed a large number of terms encompassing a large number of cellular and nuclear processes (Fisher exact test, Padj. < 0.01). Although a handful of genes in the IIS/TOR pathway including Ilp5, Rheb, and Sirt2 showed significant elevation in expression, known key genes such as InR, chico, insulin peptide genes, and the nutrient-sensing pathways were not observed.ConclusionsOur results suggest that a more diverse network of pathways and gene networks mediate the diet response in our population. These results have important implications for future studies focusing on diet responses in natural populations.

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HEPATOPROTECTIVE EFFECT OF A 70% ETHANOL EXTRACT OF GOD'S CROWN FRUIT (PHALERIA MACROCARPA) AGAINST PARACETAMOL HEPATOTOXICITY IN SWISS WEBSTER MICE

Berkala Ilmiah Kedokteran Duta Wacana ◽

10.21460/bikdw.v4i1.127 ◽

2019 ◽

Vol 4 (1) ◽

pp. 18

Author(s):

Tejo Jayadi

Keyword(s):

Hepatic Injury ◽

Ethanol Extract ◽

Positive Control ◽

Control Treatment ◽

Control Group ◽

Toxic Metabolite ◽

Toxic Dose ◽

Treatment Groups ◽

Phaleria Macrocarpa ◽

Anti Inflammatory

Background: The god’s crown fruits have properties as antioxidants and anti-inflammatory. Toxic doses of paracetamol can injure the liver through toxic metabolite bonds with cytoplasmic proteins that cause free radicals to form. The aim of this research is to know the effect of the crown of gods extracts on paracetamol hepatotoxicity. Method: A total of 30 of Webster swiss mice with a weight of ± 20 grams, age 3 months were randomly assigned to five groups, negative control, positive control, treatment 1,2 and 3. A 70% ethanol extract of god’s crown fruit given in doses 60mg, 120mg and 240mg per kgBB mice. The extract was administered for 14 days in the treatment groups, then on day 15 paracetamol ware administered in a given dose 300mg/kgBB for 1 day for the positive control group and treatment groups. On day 16, the serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels were examined from the orbital sinuses and animals terminated liver tissues taken and immediately fixed in 10% buffer formalin for histological examination. Results and Discussion: The 70% ethanol extract of the god’s crown fruits decreased blood serum levels of AST and ALT, and these results were supported by histopathologic scores of the liver in which histopathologic scores were improved with the increasing doses (p < 0.05). The secondary metabolite contents of the god’s crown fruit extract served as an antioxidant and anti-inflammatory, protecting hepatic injury from the toxic metabolite of paracetamol. Conclusion: A 70% ethanol extract of god’s crown fruit (Phaleria macrocarpa) have hepatoprotective properties that effectively prevent hepatic injury due to paracetamol toxic dose.

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Cross-species alcohol dependence-associated gene networks: Co-analysis of mouse brain gene expression and human genome-wide association data

10.1101/380584 ◽

2018 ◽

Author(s):

Kristin M. Mignogna ◽

Silviu A. Bacanu ◽

Brien P. Riley ◽

Aaron R. Wolen ◽

Michael F. Miles

Keyword(s):

Gene Expression ◽

Alcohol Dependence ◽

Mouse Brain ◽

Gene Networks ◽

Association Studies ◽

Complex Trait ◽

Genome Wide Association ◽

Model Organisms ◽

Genome Wide Association Studies ◽

Genome Wide

AbstractGenome-wide association studies on alcohol dependence, by themselves, have yet to account for the estimated heritability of the disorder and provide incomplete mechanistic understanding of this complex trait. Integrating brain ethanol-responsive gene expression networks from model organisms with human genetic data on alcohol dependence could aid in identifying dependence-associated genes and functional networks in which they are involved. This study used a modification of the Edge-Weighted Dense Module Searching for genome-wide association studies (EW-dmGWAS) approach to co-analyze whole-genome gene expression data from ethanol-exposed mouse brain tissue, human protein-protein interaction databases and alcohol dependence-related genome-wide association studies. Results revealed novel ethanol-regulated and alcohol dependence-associated gene networks in prefrontal cortex, nucleus accumbens, and ventral tegmental area. Three of these networks were overrepresented with genome-wide association signals from an independent dataset. These networks were significantly overrepresented for gene ontology categories involving several mechanisms, including actin filament-based activity, transcript regulation, Wnt and Syndecan-mediated signaling, and ubiquitination. Together, these studies provide novel insight for brain mechanisms contributing to alcohol dependence.

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AdpA Positively Regulates Morphological Differentiation and Chloramphenicol Biosynthesis in Streptomyces venezuelae

Microbiology Spectrum ◽

10.1128/spectrum.01981-21 ◽

2021 ◽

Author(s):

Małgorzata Płachetka ◽

Michał Krawiec ◽

Jolanta Zakrzewska-Czerwińska ◽

Marcin Wolański

Keyword(s):

Secondary Metabolites ◽

Morphological Differentiation ◽

Transcriptional Regulator ◽

Pleiotropic Effect ◽

Model Organisms ◽

Developmental Studies ◽

Streptomyces Venezuelae ◽

Cellular Processes

Streptomyces are well-known producers of valuable secondary metabolites which include a large variety of antibiotics and important model organisms for developmental studies in multicellular bacteria. The conserved transcriptional regulator AdpA of Streptomyces exerts a pleiotropic effect on cellular processes, including the morphological differentiation and biosynthesis of secondary metabolites.

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Phenolic Composition of Hydrophilic Extract of Manna from Sicilian Fraxinus angustifolia Vahl and its Reducing, Antioxidant and Anti-Inflammatory Activity in Vitro

Antioxidants ◽

10.3390/antiox8100494 ◽

2019 ◽

Vol 8 (10) ◽

pp. 494 ◽

Cited By ~ 5

Author(s):

Alessandro Attanzio ◽

Antonella D’Anneo ◽

Francesco Pappalardo ◽

Francesco Paolo Bonina ◽

Maria Antonia Livrea ◽

...

Keyword(s):

Disease Model ◽

Membrane Lipid ◽

In Vitro Assays ◽

Alcoholic Extract ◽

Cellular Models ◽

Reducing Ability ◽

Scavenger Activity ◽

Fraxinus Angustifolia ◽

Anti Inflammatory

Manna, a very singular vegetable product derived from the spontaneous solidification of the sap of some Fraxinus species, has long been known for its mild laxative and emollient properties. In this work, a hydro-alcoholic extract of manna (HME) from Sicilian Fraxinus angustifolia Vahl was investigated using HPLC-DAD to find phenol components and using chemical and biological in vitro assays to determine its reducing, antioxidant and anti-inflammatory capacity. We identified elenolic acid, tyrosol, hydroxytyrosol, catechin, fraxetin, verbascoside, gallic acid, procyanidin-B1, and luteolin 3,7 glucoside, in order of abundance. Measurements of total antioxidant activity by Folin-Ciocalteu reaction and ferric reducing ability (FRAP), as well as of scavenger activity towards ABTS•+, DPPH•, and perferryl-myoglobin radicals, showed that the phytocomplex effectively reduced oxidants with different standard potentials. When compared with vitamin E, HME also behaved as an efficient chain-breaking antioxidant against lipoperoxyl radicals from methyl linoleate. In cellular models for oxidative stress, HME counteracted membrane lipid oxidation of human erythrocytes stimulated by tert-butyl hydroperoxide and prevented the generation of reactive oxygen species, as well as the GSH decay in IL-1β–activated intestinal normal-like cells. Moreover, in this in vitro intestinal bowel disease model, HME reduced the release of the pro-inflammatory cytokines IL-6 and IL-8. These findings may suggest that manna acts as an antioxidant and anti-inflammatory natural product in humans, beyond its well-known effects against constipation.

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