Zebrafish Models of Kidney Damage and Repair

Mitigation of gentamycin induced acute kidney injury due to benzothiazole derivatives N1 and N5: Antioxidant and renoprotective mechanisms in-vivo zebrafish

Acute kidney injury (AKI) is marked by a rapid decline in renal function, often caused by oxidative stress and nephrotoxic agents. Complications limit current therapeutic strategies, and no specific drugs are available to prevent renal injury or accelerate recovery. In the present research, we investigated the therapeutic efficacy of synthesized 2-aminobenzothiazole derivatives, N1 and N5, in mitigating Gentamicin (Gen) -induced renal damage in vivo zebrafish. The preliminary work of radical scavenging and hemolysis inhibition assay revealed that, both compounds exhibited strong antioxidant and anti-inflammatory activities. Furthermore, acute toxicity assays in zebrafish embryo/larvae revealed no adverse effects at concentrations up to 200 μM were tested, highlighting the safety of these compounds. In the zebrafish AKI model, Gen exposure led to oxidative stress, inflammation, and impaired glomerular filtration with tissue damage. Treatment with N1 and N5 significantly reduced ROS levels, apoptosis, and lipid peroxidation and restored antioxidant enzyme activities. Furthermore, N5 treatment improved renal filtration and reduced proteinuria levels, indicating its ability to mitigate nephrotoxic effects. Gene expression analysis showed that N1 and N5 downregulated pro-inflammatory markers (cox-2, tnfα, mpo) and angiogenic mediators (vegf, vegfr2), demonstrating anti-inflammatory and anti-angiogenic properties. Histological analyses revealed that N1 and N5 attenuated glomerular and tubular damage, reduced necrosis, and promoted tissue repair. These findings highlight the potential of 2-aminothiazole derivatives as effective therapeutic agents for AKI, offering antioxidant, anti-inflammatory, and cytoprotective benefits and warranting further investigation into their long-term efficacy in chronic kidney disease models.

In Vivo Assessment of Individual and Total Proteinuria in Zebrafish Larvae Using the Solvatochromic Compound ZMB741

The robustness of blood filtration in the kidney is supported by two major functions: the molecular sieve of the glomerulus and reabsorption of the proximal tubules. Detecting glomerular dysfunction is challenging because of the compensatory nature of proximal tubule reabsorption. To facilitate pathophysiological studies of the vertebrate kidney, zebrafish pronephroi are used, owing to their simple glomerular and proximal tubular configuration. In this study, a solvatochromic dye with an affinity for plasma proteins was used to detect urinary proteins leaking into the ureter of zebrafish. Aristolochic acid exposure to fertilized eggs of transgenic zebrafish expressing green fluorescent protein from the proximal tubules to the excretory pore induced concentration-dependent renal dysfunction. The solvatochromic dye ZMB741 was applied via static immersion to analyze leaked dye-plasma-protein complexes in the ureter; their axial distribution was imaged by using confocal microscopy. The effect of resveratrol, an attenuator of aristolochic acid nephropathy, was further analyzed. This method enables individual-level analysis of podocytopathy, a mild glomerular disease that does not necessarily lead to the excretion of proteinuria. Moreover, it will be useful for pathophysiological studies of renal function and the identification of potential therapeutic drugs.

Synergistic modulation of endoplasmic reticulum stress pathway, oxidative DNA damage and apoptosis by β-amyrin and metformin in mitigating hyperglycemia-induced renal damage using adult zebrafish model

Diabetic nephropathy (DN) can be prevented with early therapeutic intervention in diabetic patients. Recent investigations suggest that β-amyrin, a pentacyclic triterpenoid, could offer significant benefits with its potential antihyperglycemic and nephroprotective effects. We investigated the protective effects of β-amyrin alone and combined it with metformin, the cornerstone therapy for diabetes, using a hyperglycemic adult Zebrafish (ZF) model. The ZF were subjected to hyperglycemia by immersing them in 111 mM glucose solutions. Treatment efficacy was assessed by measuring serum glucose and insulin levels and antioxidant, ER stress, apoptosis, and proinflammatory markers. ZF kidneys were also studied for immunohistochemistry and histopathology. Results revealed that the combined treatment of β-amyrin and metformin resulted in a significant decrease (p ≤ 0.05) in blood glucose levels to 104.54 ± 1.63 mg/dL, in comparison to 388.75 ± 4.32 mg/dL in the untreated diseased control group. The reduction in hyperglycemia was more pronounced than treatment with either compound alone. Moreover, treatment with the combination restored renal function in diseased ZF, leading to significantly lower (p ≤ 0.05) serum urea (SU: 19.57 ± 1.61 mg/dL) and serum creatinine (SC: 0.56 ± 0.02 mg/dL) values compared to treatment with β-amyrin (SU:27.02 ± 0.96 mg/dL; SC: 0.7 ± 0.01 mg/dL) or metformin (SU: 24.53 ± 1.29 mg/dL; SC: 0.6 ± 0.02 mg/dL) alone. The treatment also reduced oxidative stress markers, apoptosis and ER stress markers, and proinflammatory cytokines. Histopathological analysis showed improved renal architecture with significantly lower (p ≤ 0.05) renal tubular injury scores with the combination than with individual treatment. This study provides novel insights into the combined therapeutic effects of β-amyrin and metformin in mitigating hyperglycemia-induced renal damage through key molecular pathways, highlighting a potentially effective therapeutic strategy for diabetic nephropathy. The findings hold promising translational relevance for developing combination therapies aimed at improving clinical outcomes in diabetic nephropathy patients.

Deconvolving Passive and Active Targeting of Liposomes Bearing LDL Receptor Binding Peptides Using the Zebrafish Embryo Model

Improving target versus off-target ratio in nanomedicine remains a major challenge for increasing drug bioavailability and reducing toxicity. Active targeting using ligands on nanoparticle surfaces is a key approach but has limited clinical success. A potential issue is the integration of targeting ligands also changes the physicochemical properties of nanoparticles (passive targeting). Direct studies to understand the mechanisms of active targeting and off-targeting in vivo are limited by the lack of suitable tools. Here, the biodistribution of a representative active targeting liposome is analyzed, modified with an apolipoprotein E (ApoE) peptide that binds to the low-density lipoprotein receptor (LDLR), using zebrafish embryos. The ApoE liposomes demonstrated the expected liver targeting effect but also accumulated in the kidney glomerulus. The ldlra-/- zebrafish is developed to explore the LDLR-specificity of ApoE liposomes. Interestingly, liver targeting depends on the LDLR-specific interaction, while glomerular accumulation is independent of LDLR and peptide sequence. It is found that cationic charges of peptides and the size of liposomes govern glomerular targeting. Increasing the size of ApoE liposomes can avoid this off-targeting. Taken together, the study shows the potential of the zebrafish embryo model for understanding active and passive targeting mechanisms, that can be used to optimize the design of nanoparticles.

Metabolome evidence of CKDu risks after chronic exposure to simulated Sri Lanka drinking water in zebrafish

It is still a serious public health issue that chronic kidney disease of uncertain etiology (CKDu) in Sri Lanka poses challenges in identification, prevention, and treatment. What environmental factors in drinking water cause kidney damage remains unclear. This study aimed to investigate the risks of various environmental factors that may induce CKDu, including water hardness, fluoride (HF), heavy metals (HM), microcystin-LR (MC-LR), and their combined exposure (HFMM). The research focused on comprehensive metabolome analysis, and correlation with transcriptomic and gut microbiota changes. Results revealed that chronic exposure led to kidney damage and pancreatic toxicity in adult zebrafish. Metabolomics profiling showed significant alterations in biochemical processes, with enriched metabolic pathways of oxidative phosphorylation, folate biosynthesis, arachidonic acid metabolism, FoxO signaling pathway, lysosome, pyruvate metabolism, and purine metabolism. The network analysis revealed significant changes in metabolites associated with renal function and diseases, including 20-Hydroxy-LTE4, PS(18:0/22:2(13Z,16Z)), Neuromedin N, 20-Oxo-Leukotriene E4, and phenol sulfate, which are involved in the fatty acyls and glycerophospholipids class. These metabolites were closely associated with the disrupted gut bacteria of g_ZOR0006, g_Pseudomonas, g_Tsukamurella, g_Cetobacterium, g_Flavobacterium, which belonged to dominant phyla of Firmicutes and Proteobacteria, etc., and differentially expressed genes (DEGs) such as egln3, ca2, jun, slc2a1b, and gls2b in zebrafish. Exploratory omics analyses revealed the shared significantly changed pathways in transcriptome and metabolome like calcium signaling and necroptosis, suggesting potential biomarkers for assessing kidney disease.

Standardization of zebrafish drug testing parameters for muscle diseases

Skeletal muscular diseases predominantly affect skeletal and cardiac muscle, resulting in muscle weakness, impaired respiratory function and decreased lifespan. These harmful outcomes lead to poor health-related quality of life and carry a high healthcare economic burden. The absence of promising treatments and new therapies for muscular disorders requires new methods for candidate drug identification and advancement in animal models. Consequently, the rapid screening of drug compounds in an animal model that mimics features of human muscle disease is warranted. Zebrafish are a versatile model in preclinical studies that support developmental biology and drug discovery programs for novel chemical entities and repurposing of established drugs. Due to several advantages, there is an increasing number of applications of the zebrafish model for high-throughput drug screening for human disorders and developmental studies. Consequently, standardization of key drug screening parameters, such as animal husbandry protocols, drug compound administration and outcome measures, is paramount for the continued advancement of the model and field. Here, we seek to summarize and explore critical drug treatment and drug screening parameters in the zebrafish-based modeling of human muscle diseases. Through improved standardization and harmonization of drug screening parameters and protocols, we aim to promote more effective drug discovery programs.

Elucidating environmental factors and their combined effects on CKDu in Sri Lanka using zebrafish

Chronic kidney disease with uncertain etiology (CKDu) in Sri Lanka has attracted much attention as a global health issue. However, how environmental factors in local drinking water induce kidney damage in organisms is still elusive. We investigated multiple environmental factors including water hardness and fluoride (HF), heavy metals (HM), microcystin-LR (MC-LR), and their combined exposure (HFMM) to elucidate their toxic effects on CKDu risk in zebrafish. Acute exposure affected renal development and inhibited the fluorescence of Na, K-ATPase alpha1A4:GFP zebrafish kidney. Chronic exposure influenced the body weight of both genders of adult fish and induced kidney damage by histopathological analyses. Furthermore, the exposure significantly disturbed differential expression genes (DEGs), diversity and richness of gut microbiota, and critical metabolites related to renal functions. The transcriptomic analysis revealed that kidney-related DEGs were linked with renal cell carcinoma, proximal tubule bicarbonate reclamation, calcium signaling pathway, and HIF-1 signaling pathway. The significantly disrupted intestinal microbiota was closely related to the environmental factors and H&E score, which demonstrated the mechanisms of kidney risks. Notably, the Spearman correlation analysis indicated that the changed bacteria such as Pseudomonas, Paracoccus, and ZOR0006, etc were significantly connected to the DEGs and metabolites. Therefore, the assessment of multiple environmental factors provided new insights on "bio-markers" as potential therapies of the target signaling pathways, metabolites, and gut bacteria to monitor or protect residents from CKDu.

Effectiveness of zebrafish models in understanding human diseases-A review of models

Understanding the detailed mechanism behind every human disease, disorder, defect, and deficiency is a daunting task concerning the clinical diagnostic tools for patients. Hence, a closely resembling living or simulated model is of paramount interest for the development and testing of a probable novel drug for rectifying the conditions pertaining to the various ailments. The animal model that can be easily genetically manipulated to suit the study of the therapeutic motive is an indispensable asset and within the last few decades, the zebrafish models have proven their effectiveness by becoming such potent human disease models with their use being extended to various avenues of research to understand the underlying mechanisms of the diseases. As zebrafish are explored as model animals in understanding the molecular basis and genetics of many diseases owing to the 70% genetic homology between the human and zebrafish genes; new and fascinating facts about the diseases are being surfaced, establishing it as a very powerful tool for upcoming research. These prospective research areas can be explored in the near future using zebrafish as a model. In this review, the effectiveness of the zebrafish as an animal model against several human diseases such as osteoporosis, atrial fibrillation, Noonan syndrome, leukemia, autism spectrum disorders, etc. has been discussed.

Zebrafish (Danio rerio) as a model organism for screening nephrotoxic chemicals and related mechanisms

Because of essential role in homeostasis of the body fluid and excretion of wastes, kidney damage can lead to severe impacts on health and survival of humans. For most chemicals, nephrotoxic potentials and associated mechanisms are unclear. Hence, fast and sensitive screening measures for nephrotoxic chemicals are required. In this study, the utility of zebrafish (Danio rerio) was evaluated for the investigation of chemical-induced kidney toxicity and associated modes of toxicity, based on the literature review. Zebrafish has a well-understood biology, and many overlapping physiological characteristics with mammals. One such characteristic is its kidneys, of which histology and functions are similar to those of mammals, although unique differences of zebrafish kidneys, such as kidney marrow, should be noted. Moreover, the zebrafish kidney is simpler in structure and easy to observe. For these advantages, zebrafish has been increasingly used as an experimental model for screening nephrotoxicity of chemicals and for understanding related mechanisms. Multiple endpoints of zebrafish model, from functional level, i.e., glomerular filtration, to transcriptional changes of key genes, have been assessed to identify chemical-induced kidney toxicities, and to elucidate underlying mechanisms. The most frequently studied mechanisms of chemical-induced nephrotoxicity in zebrafish include oxidative stress, inflammation, DNA damage, apoptosis, fibrosis, and cell death. To date, several pharmaceuticals, oxidizing agents, natural products, biocides, alcohols, and consumer chemicals have been demonstrated to exert different types of kidney toxicities in zebrafish. The present review shows that zebrafish model can be efficiently employed for quick and reliable assessment of kidney damage potentials of chemicals, and related toxic mechanisms. The toxicological information obtained from this model can be utilized for identification of nephrotoxic chemicals and hence for protection of public health.

Sulphated polysaccharide from Sargassum myriocystum confers protection against gentamicin-induced nephrotoxicity in adult zebrafish

The beneficial effect of purified fraction of sulphated polysaccharide extracted from Sargassum myriocystum (SMP) was examined on the gentamicin-induced nephrotoxicity in adult zebrafish. The major purified fractions (SMP1, SMP2 and SMP3) were obtained by anion-exchange and size-exclusion chromatography and characterized by FTIR, GCMS and NMR. The in vitro antioxidant activities of all purified SMP fractions were analysed. The SMP2 showed maximum carbohydrate, sulphate and fucose content with strong antioxidant activity than other fractions. Further, we evaluated the efficacy of SMP2 against gentamicin-induced nephrotoxicity in zebrafish model. The SMP2 administered group showed a significant attenuation in oxidative stress and histopathological alterations observed in renal tissues of gentamicin treated group. Moreover, the SMP2 supressed renal mRNA expression levels of KIM-1, NF-κB, TNF-α and IL-6 in dose-dependent manner. Thus, the present study suggests that the SMP2 is a potent antioxidant with anti-inflammatory and renoprotective properties that ameliorated the GEN induced nephrotoxicity in adult zebrafish.

Do Zebrafish Obey Lipinski Rules?

The use of zebrafish in whole organism phenotypic assays has become a valuable strategy throughout the drug discovery process. Zebrafish assays can be used not only to screen libraries of compounds at the earliest stages but also to evaluate advanced leads for their effects on specific biological pathways or for toxicity. However, when confronted with inactivity of a compound in a zebrafish assay, there are little data that can be used to judge if the compound is truly biologically inert or inactive due to a lack of permeability into the model organism. While medicinal chemistry principles suggest parameters that are predictive of human oral bioavailability, cellular permeability, and even bacterial permeability, there have been no such parameters developed for zebrafish absorption. To address this question, we compiled a set of 700 compounds reported in the literature to be active in zebrafish assays, evaluated their properties, and compared them to properties derived from a set of historical drugs and a set of recently approved oral drugs. While some properties overlap, the averages and 10th and 90th percentiles of molecular weight, octanol-water partition coefficient (logP), H-bond counts, and polar surface area for zebrafish-active compounds are statistically different from those of known drugs. This analysis should be useful to scientists interpreting structure-activity relationships based on data from zebrafish assays and help to inform the translation from fish to mammals.

Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish

Background

Zebrafish is a full-developed model system for studying development processes and human disease. Recent studies of deep sequencing had discovered a large number of long non-coding RNAs (lncRNAs) in zebrafish. However, only few of them had been functionally characterized. Therefore, how to take advantage of the mature zebrafish system to deeply investigate the lncRNAs’ function and conservation is really intriguing.

Results

We systematically collected and analyzed a series of zebrafish RNA-seq data, then combined them with resources from known database and literatures. As a result, we obtained by far the most complete dataset of zebrafish lncRNAs, containing 13,604 lncRNA genes (21,128 transcripts) in total. Based on that, a co-expression network upon zebrafish coding and lncRNA genes was constructed and analyzed, and used to predict the Gene Ontology (GO) and the KEGG annotation of lncRNA. Meanwhile, we made a conservation analysis on zebrafish lncRNA, identifying 1828 conserved zebrafish lncRNA genes (1890 transcripts) that have their putative mammalian orthologs. We also found that zebrafish lncRNAs play important roles in regulation of the development and function of nervous system; these conserved lncRNAs present a significant sequential and functional conservation, with their mammalian counterparts.

Conclusions

By integrative data analysis and construction of coding-lncRNA gene co-expression network, we gained the most comprehensive dataset of zebrafish lncRNAs up to present, as well as their systematic annotations and comprehensive analyses on function and conservation. Our study provides a reliable zebrafish-based platform to deeply explore lncRNA function and mechanism, as well as the lncRNA commonality between zebrafish and human.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4458-7) contains supplementary material, which is available to authorized users.

The Efficacy of Puromycin and Adriamycin for Induction of Glomerular Failure in Larval Zebrafish Validated by an Assay of Glomerular Permeability Dynamics

Defects in the glomerular filtration barrier (GFB) play a major role in the onset of human renal diseases. Highly ramified glomerular cells named podocytes are a critical component of the GFB. Injury to podocytes results in abnormal excretion of plasma proteins, which can lead to chronic kidney disease. The conserved paired nephron of larval zebrafish is an excellent model for assessing glomerular function and injury. The efficacy of two known podocyte toxins was tested to refine models of acute podocyte injury in larval zebrafish. The validated compound was then used to test a novel assay of the dynamics of abnormal protein excretion. Injected adriamycin was found to be unsuitable for induction of glomerular injury due to off-target cardiovascular toxicity. In contrast, puromycin treatment resulted in a loss of discriminative filtration, measured by excretion of 70 kDa dextran, and podocyte effacement confirmed by electron microscopy. The dynamics of dextran excretion during puromycin injury modeled the onset of glomerular damage within 24 hours postinjection. These data validate puromycin for induction of acute podocyte injury in zebrafish larvae and describe a semihigh-throughput assay for quantifying the dynamics of abnormal protein excretion.