Transparent adult zebrafish as a tool for in vivo transplantation analysis

Development of sensorimotor responses in larval zebrafish: A comparison between wild-type and GCaMP6s transgenic line

During early development, zebrafish larvae exhibit stereotypical behaviors, which rapidly become more complex. Thus, generating mutant transgenic lines that maintain transparency throughout their larval stage and that can be used to record brain activity has offered strategic opportunities to investigate the underlying neural correlates of behavior establishment. However, few studies have documented the sensorimotor profile of these lines during larval development. Here, we set up a behavioral characterization using diverse stimuli (light and vibration) throughout larval development to compare the responses of a transgenic strain expressing a pan-neuronal calcium indicator (GCaMP6s) with that of a wild-type strain. Interestingly, we report a drastic switch in behavioral responses to light transitions at 11 days post-fertilization (dpf) and to vibration stimuli at 14 dpf in both lines. These data highlight a specific time window representing an increase in behavioral complexity. Meanwhile, we found some differences in the maturation of sensorimotor responses between GCaMP6s and wild-type strains. Although some of these differences are minor, they highlight the need for careful attention when using mutant/transgenic lines for behavioral studies. Overall, our results support using GCaMP6s strain in investigating the neural mechanisms underlying the developmental maturation of sensorimotor responses.

An LNP-mRNA vaccine protects fish against rhabdovirus infection

mRNA vaccines are poised to revolutionize disease prevention, following the approval of their administration to humans against SARS-CoV-2. Although they have been extensively studied for human applications, their potential in the veterinary field has not been explored yet. No mRNA vaccines have yet been reported for fish, despite the urgent need for new vaccines against emerging pathogens in aquaculture. As fish are ectotherms, temperature has an impact on their immune response and on many other biological parameters, including the composition of membrane lipids. It is therefore crucial to identify whether mRNA delivery systems are suitable for in vivo expression in fish for vaccine purposes. In the present study, we developed a proof of concept for mRNA vaccination in rainbow trout, a salmonid, demonstrating the efficacy of current vaccine delivery systems in fish. We used lipid nanoparticles (LNPs), which represent the most advanced delivery technology for mRNA. LNPs use a combination of lipid components that form an encapsulating structure offering protection and promote endosome escape of the mRNA to allow its expression. In vitro assays showed that LNPs are a powerful vehicle for mRNA delivery in fish cells without substantial toxicity. In vivo imaging in adult zebrafish (Danio rerio) demonstrated that intramuscular injection of LNP-formulated egfp mRNA resulted in local expression of eGFP for up to 7 days. An LNP-based mRNA vaccine candidate encoding the viral haemorrhagic septicaemia virus (VHSV) glycoprotein induced neutralizing antibodies in rainbow trout (Oncorhynchus mykiss) and offers almost complete protection against a lethal viral challenge. Our data constitute a first proof of concept of mRNA vaccination in fish, paving the way for new developments in veterinary vaccines for aquaculture.

tp53 R217H and R242H mutant zebrafish exhibit dysfunctional p53 hallmarks and recapitulate Li-Fraumeni syndrome phenotypes

Li-Fraumeni syndrome (LFS) is a hereditary cancer predisposition syndrome associated with a highly penetrant cancer spectrum characterized by germline TP53 mutations. We characterized the first LFS zebrafish hotspot mutants, tp53 R217H and R242H (human R248H and R273H), and found these mutants exhibit partial-to-no activation of p53 target genes, have defective cell-cycle checkpoints, and display partial-to-full resistance to apoptosis, although the R217H mutation has hypomorphic characteristics. Spontaneous tumor development histologically resembling human sarcomas was observed as early as 6 months. tp53 R242H mutants had a higher lifetime tumor incidence compared to tp53 null and R217H mutants, suggesting it is a more aggressive mutation. We observed mutation-specific tumor phenotypes across tp53 mutants with associated diverse transcriptomic and DNA methylome profiles in tp53 mutant larvae, impacting metabolism, cell signalling, and biomacromolecule synthesis and degradation. These tp53 zebrafish mutants demonstrate fidelity to their human counterparts and provide new insights into underlying tumorigenesis mechanisms and kinetics that suggest metabolic rewiring and cellular signalling changes occur prior to tumor initiation, which will guide targeted therapeutics for LFS.

Potential of Garra rufa as a novel high-temperature resistant model fish: a review on current and future approaches

Garra rufa, commonly known as the "doctor fish", is a freshwater cyprinid native to warm regions of the Middle East. Since the late twentieth century, it has been widely utilized in spas for alternative therapeutics and fish pedicures (or manicures) for dermatological diseases such as psoriasis and eczema. Owing to its unique characteristics, there is growing interest in exploring various applications of G. rufa. This review provides a comprehensive summary of the phylogenetic position, ecology, biological characteristics, and breeding methods of G. rufa, and provides insights into its use as a therapeutic fish. Notably, the ability of G. rufa to thrive in high-temperature environments exceeding 37 °C distinguishes it from other cyprinids and suggests its potential as a model for human diseases, such as human infectious diseases, and in use in cancer xenograft models for high-throughput drug screening. The ongoing genome sequencing project for G. rufa aims to elucidate the mechanisms underlying its high-temperature tolerance and offers valuable genomic resources. These efforts have resulted in significant advances in fish aquaculture, species conservation, and biomedical research.

Uncovering the pathogenic mechanisms of Cronobacter turicensis: A dual transcriptomics study using a zebrafish larvae model

PURPOSE

Cronobacter (C.) is an emerging opportunistic pathogen representing a significant cause of mortality in neonatal patients with bacteremia and meningitis. The pathobiology of Cronobacter mediated meningitis has primarily been investigated using in vitro models. In this study, we used zebrafish to investigate in vivo the infection strategy of the sepsis/meningitis-causing strain C. turicensis z3032 (LMG 23827T) and the immune response of zebrafish larvae after central nervous system (CNS) invasion. Global gene expression profiles of both organisms were analyzed using RNA-Seq.

METHODS

Injection of bacteria into the yolk sac resulted in proliferation of bacteria and translocation to different tissues, including the brain. Infected larval heads were obtained by microdissection and dual RNA-sequencing was performed on host and pathogen simultaneously.

RESULTS

A total of 1432 genes in C. turicensis z3032 and 80 genes in zebrafish were found to be differentially expressed. Upregulated virulence genes in C. turicensis included those encoding for denitrification and anaerobic respiration, chemotaxis, surface structures, and secretion systems. In zebrafish, transcriptional changes included inflammatory processes, cytokine mediated signaling pathways, and NF-kB signaling as the primary GO categories for upregulated genes in response to infection.

CONCLUSION

The dual transcriptomics approach provided a unique opportunity to create a comprehensive catalog of differentially expressed genes in both the pathogen and the host, offering new insights into the infection strategies of C. turicensis and zebrafish immune response.

Imaging of cellular dynamics from a whole organism to subcellular scale with self-driving, multiscale microscopy

Most biological processes, from development to pathogenesis, span multiple time and length scales. While light-sheet fluorescence microscopy has become a fast and efficient method for imaging organisms, cells and subcellular dynamics, simultaneous observations across all these scales have remained challenging. Moreover, continuous high-resolution imaging inside living organisms has mostly been limited to a few hours, as regions of interest quickly move out of view due to sample movement and growth. Here, we present a self-driving, multiresolution light-sheet microscope platform controlled by custom Python-based software, to simultaneously observe and quantify subcellular dynamics in the context of entire organisms in vitro and in vivo over hours of imaging. We apply the platform to the study of developmental processes, cancer invasion and metastasis, and we provide quantitative multiscale analysis of immune-cancer cell interactions in zebrafish xenografts.

The G-protein coupled receptor OXER1 is a tissue redox sensor essential for intestinal epithelial barrier integrity

Generation of reactive oxygen species is an important part of the innate immune response. Generating microbicidal levels of reactive oxygen species (ROS) requires adaptation of mucosal barriers. High tolerance of ROS provides improved innate immune defenses against pathogens, whereas low tolerance renders host cells prone to chronic toxicity and mutagenesis, which can promote inflammation (e.g., in asthma and Crohn's disease) and cancerogenesis. The mechanisms that sense and mediate host tolerance to ROS are little understood. In this study, we discover an unexpected role for the redox-sensitive, chemokine-like lipid 5-oxo-eicosatetraenoic acid (5-KETE) in redox adaptation. 5-KETE is known to attract leukocytes to damaged/infected mucosal barriers by signaling through its receptor, OXER1. Suggestive of a distinct non-immune function, we here report that the loss of the OXER1 ortholog Hcar1-4 causes barrier defects and baseline inflammation in the intestine of live zebrafish larvae. In zebrafish and cultured human cells, OXER1 signaling protects against oxidative nucleotide lesions by inducing DNA-protective Nudix hydrolases. Our data reveal the oxoeicosanoid pathway as a conserved ROS resilience mechanism that fortifies pathogen-exposed mucosal linings against increased oxidative stress in vivo.

DHRS7 Integrates NADP+/NADPH Redox Sensing with Inflammatory Lipid Signalling via the Oxoeicosanoid Pathway

During the innate immune response at epithelial wound sites, oxidative stress acts microbicidal and-mechanistically less well understood-as an immune and resilience signal. The reversible sulfhydryl (SH) oxidation of kinases, phosphatases, and transcription factors constitute the perhaps best-known redox signalling paradigm, whereas mechanisms that transduce metabolic redox cues, such as redox cofactor balance, remain little explored. Here, using mammalian cells, microsomes, and live zebrafish, we identify DHRS7, a short-chain fatty acid dehydrogenase/reductase (SDR), as conserved, 5-hydroxyeicosanoid dehydrogenase (5-HEDH). Under oxidative stress, DHRS7 consumes NADP+ to convert arachidonic acid (AA)-derived 5(S)-HETE into the inflammatory lipid 5-KETE, which activates leukocyte chemotaxis via the OXER1 receptor. While Dhrs7 acts as a NADPH-dependent 5-KETE sink in unstressed, healthy tissue, it promotes rapid, 5-KETE dependent leukocytic inflammation in wounded zebrafish skin. Thus, DHRS7 epitomizes an underappreciated mode of redox signalling-beyond classic SH oxidation-that leverages NADPH metabolism to generate or quench a paracrine lipid signal. Metabolic redox sensors like DHRS7 might be promising therapeutic targets in diseases characterized by disturbed redox balance.

Clostridioides difficile infection study models and prospectives for probing the microbe-host interface

Clostridioides difficile infection (CDI) is an urgent public health threat with a high rate of recurrence and limited treatment options. In vivo models have been indispensable in understanding CDI pathophysiology and establishing treatment protocols and continue to be essential in pre-clinal testing. More importantly, in vivo models offer the opportunity to probe the complex systemic host response to the microbe, which is impossible to recapitulate in vitro. Nonetheless, constraints related to the availability of animal models, cost, ethical considerations, and regulatory control limit their accessibility for basic research. Furthermore, physiological and habitual divergences between animal models and humans often result in poor translatability to human patients. In addition to being more accessible, in vitro CDI models offer more control over experimental parameters and allow dynamic analysis of early infection. In vitro fermentation offers models for probing microbe-microbe and microbe-microbiome interactions, while continuous multi-stage platforms allow opportunities to study C. difficile pathophysiology and treatment in context with human-derived microbiota. However, these platforms are not suitable for probing the host-pathogen interface, leaving the challenge of modeling early CDI unanswered. As a result, alternative in vitro co-culture platforms are being developed. This review evaluates the strengths and weaknesses of each approach, as well as future directions for C. difficile research.

The Matrix of Mitochondrial Imaging: Exploring Spatial Dimensions

Mitochondria play a crucial role in human biology, affecting cellular processes at the smallest spatial scale as well as those involved in the functionality of the whole system. Imaging is the most important research tool for studying the fundamental role of mitochondria across these diverse spatial scales. A wide array of available imaging techniques have enabled us to visualize mitochondrial structure and behavior, as well as their effect on cells and tissues in a range from micrometers to centimeters. Each of the various imaging techniques that are available offers unique advantages tailored to specific research needs. Selecting an appropriate technique suitable for the scale and application of interest is therefore crucial, but can be challenging due to the large range of possibilities. The aim of this review is two-fold. First, we provide an overview of the available imaging techniques and discuss their strengths and limitations for applications across the sub-mitochondrial, cellular, tissue and organ levels for the imaging of mitochondria. Second, we identify opportunities for novel applications and advancement in the field. We emphasize the importance of integration across scales in mitochondrial imaging studies, particularly to bridge the gap between microscopic and non-invasive techniques. While integrating these diverse scales is challenging, primarily because such multi-scale approaches require expertise that spans different imaging modalities, we argue that integration has the potential to provide groundbreaking insights into mitochondrial biology. By providing a comprehensive overview of imaging techniques, this review paves the way for multi-scale imaging initiatives in mitochondrial research.

Ketamine induces plasticity in a norepinephrine-astroglial circuit to promote behavioral perseverance

Transient exposure to ketamine can trigger lasting changes in behavior and mood. We found that brief ketamine exposure causes long-term suppression of futility-induced passivity in larval zebrafish, reversing the "giving-up" response that normally occurs when swimming fails to cause forward movement. Whole-brain imaging revealed that ketamine hyperactivates the norepinephrine-astroglia circuit responsible for passivity. After ketamine washout, this circuit exhibits hyposensitivity to futility, leading to long-term increased perseverance. Pharmacological, chemogenetic, and optogenetic manipulations show that norepinephrine and astrocytes are necessary and sufficient for ketamine's long-term perseverance-enhancing aftereffects. In vivo calcium imaging revealed that astrocytes in adult mouse cortex are similarly activated during futility in the tail suspension test and that acute ketamine exposure also induces astrocyte hyperactivation. The cross-species conservation of ketamine's modulation of noradrenergic-astroglial circuits and evidence that plasticity in this pathway can alter the behavioral response to futility hold promise for identifying new strategies to treat affective disorders.

New insights into the regulation of cyp3a65 expression in transgenic tg(cyp3a65:GFP) zebrafish embryos

Facing the need for alternative models allowing assessment of metabolic-endocrine disrupting chemicals (MDCs), especially in poorly investigated tissues such as the intestine, we recently developed a transgenic zebrafish embryo in vivo model, tg(cyp3a65:GFP), expressing the Green Fluorescent Protein (GFP) under the control of the zebrafish cyp3a65 promoter, ortholog of human cyp3a4, a gene coding for a key enzyme of intestinal xenobiotic and endobiotic metabolism. In this study, we aimed to better understand the regulation of cyp3a65 expression by zfPXR, zfAhR2, and zfGR zebrafish orthologs of well-known human xenosensors PXR and AhR, and steroid nuclear receptor GR. For this purpose, we performed zebrafish embryo tg(cyp3a65:GFP) (co)exposures to a variety of agonists (clotrimazole, TCDD, fluticasone propionate) and antagonists (econazole nitrate, CH223181, RU486), which were characterized using in vitro zebrafish reporter gene assays. We show that zfPXR and zfAhR2 cooperate to positively regulate cyp3a65 expression, involving different transcription factors and their interaction. Moreover, for the first time, we show that zfGR agonist strongly inhibits the constitutive expression of cyp3a65, and we hypothesized the possible involvement of the transcriptional factor zfHNF4α. These results provide a better understanding of the regulation of zebrafish cyp3a65 expression, highlighting the complex interaction between different transcription factors, which is consistent with the multiple regulatory pathways of cyp3a4 in humans. Our data support the idea that this gene is a target of multiple contaminants capable of interacting with zfPXR, zfAhR2 and zfGR and highlights the relevance of the tg(cyp3a65:GFP) model to screen chemicals potentially acting as MDCs based on their modes of action at the intestinal level, which could be relevant for hazard assessment of chemicals for human and environmental health.

Ilicicolin C suppresses the progression of prostate cancer by inhibiting PI3K/AKT/mTOR pathway

Aberrant activation of the PI3K/AKT pathway is a driving factor in the development of prostate cancer. Therefore, inhibiting the function of the PI3K/AKT signaling pathway is a strategy for the treatment of prostate cancer. Ilicicolin C is an ascochlorin derivative isolated from the coral-derived fungus Acremonium sclerotigenum GXIMD 02501. Which has anti-inflammatory activity, but its activity against prostate cancer has not yet been elucidated. MTT assay, plate clone-formation assay, flow cytometry and real-time cell analysis technology were used to detect the effects of ilicicolin C on cell viability, proliferation, apoptosis and migration of prostate cancer cells. Molecular docking software and surface plasmon resonance technology were used to analyze the interaction between ilicicolin C and PI3K/AKT proteins. Western blot assay was performed to examine the changes in protein expression. Finally, QikProp software was used to simulate the process of ilicicolin C in vivo, and a zebrafish xenograft model was used to further verify the anti-prostate cancer activity of ilicicolin C in vivo. Ilicicolin C showed cytotoxic effects on prostate cancer cells, with the most significant effect on PC-3 cells. Ilicicolin C inhibited proliferation and migration of PC-3 cells. It could also block the cell cycle and induce apoptosis in PC-3 cells. In addition, ilicicolin C could bind to PI3K/AKT proteins. Furthermore, ilicicolin C inhibited the expression of PI3K, AKT and mTOR proteins and could also regulate the expression of downstream proteins in the PI3K/AKT/mTOR signaling pathway. Moreover, the calculations speculated that ilicicolin C was well absorbed orally, and the zebrafish xenograft model confirmed the in vivo anti-prostate cancer effect of ilicicolin C. Ilicicolin C emerges as a promising marine compound capable of inducing apoptosis of prostate cancer cells by counteracting the aberrant activation of PI3K/AKT/mTOR, suggesting that ilicicolin C may be a viable candidate for anti-prostate cancer drug development. These findings highlight the potential of ilicicolin C against prostate cancer and shed light on its mechanism of action.

Neurological function is restored post-ischemic stroke in zebrafish, with aging exerting a deleterious effect on its pathology

Ischemic stroke (IS) is a pathological condition characterized by the cessation of blood flow due to factors such as thrombosis, inflicting severe damage to the cranial nervous system and resulting in numerous disabilities including memory impairments and hemiplegia. Despite the critical nature of this condition, therapeutic options remain limited, with a pressing challenge being the development of treatments aimed at restoring neurological function. In this study, we leveraged zebrafish, renowned for their exceptional regenerative capabilities, to analyze the pathology of IS and the subsequent recovery process. We induced photothrombosis in the telencephalon utilizing rose bengal and conducted a temporal investigation of changes in cerebral vascular function and learning ability. Our findings revealed that blood flow in young zebrafish was restored approximately 7 days post-IS induction (dpi), with brain function recuperating by 14 dpi. Furthermore, we observed an escalation in the expression of the neural stem marker gene at 3dpi, followed by an upregulation of the differentiated neuron marker at 7 and 14dpi. In the aged IS model, symptoms were exacerbated. While cerebral blood flow was restored in 7 days, similar to young zebrafish, the recovery of learning ability was protracted in aged fish. Moreover, an upregulation of the differentiated neuron marker seen in young fish was not observed in the aged model. Collectively, our analysis of the zebrafish IS model and its comparison with existing rodent models may lay the groundwork for novel IS treatment strategies. Furthermore, the zebrafish IS model may prove beneficial for analyzing the impact of aging on the pathology of IS and the recovery process.

New Progress in Zebrafish Liver Tumor Models: Techniques and Applications in Hepatocellular Carcinoma Research

Liver tumors represent a serious clinical health problem that threatens human life. Previous studies have demonstrated that the pathogenesis of liver tumors is complex and influenced by various factors, highlighting limitations in both basic pathological research and clinical treatment. Traditional research methods often begin with the discovery of phenomena and gradually progress to the development of animal models and human trials. Among these, liver tumor animal models play a critical role in advancing related research. The zebrafish liver closely resembles the human liver in structure, function, and regenerative capacity. Additionally, the high transparency and rapid development of zebrafish embryos and larvae make them ideal model organisms for studying liver tumors. This review systematically summarizes recent methods for constructing zebrafish liver tumor models, including transplantation, transgenesis, induction, and gene knockout. Furthermore, the present paper explores the applications of these models in the study of liver cancer pathogenesis, metastasis, the tumor microenvironment, drug screening, and other related areas. By comparing the advantages and limitations of various models and integrating their distinct characteristics, this review provides insights for developing a novel liver tumor model that better aligns with clinical needs. This approach will offer valuable reference information for further in-depth studies of the pathological mechanisms of liver tumors and the development of new therapeutic drugs or strategies.

Investigating the Effect and Potential Mechanism of Rhamnetin 3-O-α-Rhamnoside on Acute Liver Injury In Vivo and In Vitro

Background/Objectives: Rhamnetin 3-O-α-rhamnoside (ARR) is a major flavonoid of the herb Loranthus tanakae Franch. & Sav., which has been used for treating liver diseases in China. However, the protective effect of ARR on the liver has not been reported. Methods: Zebrafish larvae were used as a visual animal model, and liver injury was induced by thioacetamide (TAA) for an acute liver injury (ALI) model. The hepatoprotective activity of ARR was evaluated by assessing liver morphology, liver function indices, oxidative stress, and the mRNA expression levels of inflammation-related genes in the zebrafish model. Additionally, the ROS level, inflammatory factors, and protein expression related to the IKKβ/NF-κB signaling pathway were measured to investigate a potential mechanism of ARR in HepG2 cells. Results: ARR ameliorated TAA-induced growth retardation, reduced liver injury phenotypes, and decreased oxidative stress in the zebrafish. ARR was also able to lower ROS levels in HepG2 cells, effectively inhibit the overactivation of the IKKβ/NF-κB signaling pathway in pathological conditions, inhibit NF-κB p65 translocation from the cytoplasm to the nucleus, and reduce the release of intracellular inflammatory factors. Conclusions: ARR showed significant protective activity against TAA-induced liver injury in in vivo and in vitro models, and its potential mechanism was closely related to the IKKβ/NF-κB signaling pathway.

Cross-species analyses of thymic mimetic cells reveal evolutionarily ancient origins and both conserved and species-specific elements

Thymic mimetic cells are molecular hybrids between medullary-thymic-epithelial cells (mTECs) and diverse peripheral cell types. They are involved in eliminating autoreactive T cells and can perform supplementary functions reflective of their peripheral-cell counterparts. Current knowledge about mimetic cells derives largely from mouse models. To provide the high resolution that proved revelatory for mice, we performed single-cell RNA sequencing on purified mimetic-cell compartments from human pediatric donors. The single-cell profiles of individual donors were surprisingly similar, with diversification of neuroendocrine subtypes and expansion of the muscle subtype relative to mice. Informatic and imaging studies on the muscle-mTEC population highlighted a maturation trajectory suggestive of skeletal-muscle differentiation, some striated structures, and occasional cellular groupings reminiscent of neuromuscular junctions. We also profiled thymic mimetic cells from zebrafish. Integration of data from the three species identified species-specific adaptations but substantial interspecies conservation, highlighting the evolutionarily ancient nature of mimetic mTECs. Our findings provide a landscape view of human mimetic cells, with anticipated relevance in autoimmunity.

The role of the haematopoietic stem cell niche in development and ageing

Blood production depends on rare haematopoietic stem cells (HSCs) and haematopoietic stem and progenitor cells (HSPCs) that ultimately take up residence in the bone marrow during development. HSPCs and HSCs are subject to extrinsic regulation by the bone marrow microenvironment, or niche. Studying the interactions between HSCs and their niche is critical for improving ex vivo culturing conditions and genetic manipulation of HSCs, which is pivotal for improving autologous HSC therapies and transplantations. Additionally, understanding how the complex molecular network in the bone marrow is altered during ageing is paramount for developing novel therapeutics for ageing-related haematopoietic disorders. HSCs are unique amongst stem and progenitor cell pools in that they engage with multiple physically distinct niches during their ontogeny. HSCs are specified from haemogenic endothelium in the aorta, migrate to the fetal liver and, ultimately, colonize their final niche in the bone marrow. Recent studies employing single-cell transcriptomics and microscopy have identified novel cellular interactions that govern HSC specification and engagement with their niches throughout ontogeny. New lineage-tracing models and microscopy tools have raised questions about the numbers of HSCs specified, as well as the functional consequences of HSCs interacting with each developmental niche. Advances have also been made in understanding how these niches are modified and perturbed during ageing, and the role of these altered interactions in haematopoietic diseases. In this Review, we discuss these new findings and highlight the questions that remain to be explored.

Strongly absorbing molecules make tissue transparent: a new insight for understanding tissue optical clearing

Optical imaging plays a central role in the field of biomedicine, but it suffers from the light scattering of tissues. The research group from Stanford University has reported a counterintuitive observation that strongly absorbing molecules could achieve optical transparency in live animals, providing a new insight for understanding tissue optical clearing. It empowers scientists to leverage optical imaging techniques for in vivo observation of a wide range of deep-seated structures and activities.

Automated In Vivo Phenotypic Screening Platform for Identifying Factors that Affect Cell Regeneration Kinetics

Various strategies for replacing retinal neurons lost in degenerative diseases are under investigation, including stimulating the endogenous regenerative capacity of Müller Glia (MG) as injury-inducible retinal stem cells. Inherently regenerative species, such as zebrafish, have provided key insights into mechanisms regulating MG dedifferentiation to a stem-like state and the proliferation of MG and MG-derived progenitor cells (MGPCs). Interestingly, promoting MG/MGPC proliferation is not sufficient for regeneration, yet mechanistic studies are often focused on this measure. To fully account for the regenerative process, and facilitate screens for factors regulating cell regeneration, an assay for quantifying cell replacement is required. Accordingly, we adapted an automated reporter-assisted phenotypic screening platform to quantify the pace of cellular regeneration kinetics following selective cell ablation in larval zebrafish. Here, we detail a method for using this approach to identify chemicals and genes that control the rate of retinal cell regeneration following selective retinal cell ablation.

Neuroblastoma-derived hypoxic extracellular vesicles promote metastatic dissemination in a zebrafish model

The zebrafish (Danio rerio) is a valuable model organism for studying human biology due to its easy genetic manipulation and small size. It is optically transparent and shares genetic similarities with humans, making it ideal for studying developmental processes, diseases, and drug screening via imaging-based approaches. Solid malignant tumors often contain hypoxic areas that stimulate the release of extracellular vesicles (EVs), lipid-bound structures released by cells into the extracellular space, that facilitate short- and long-range intercellular communication and metastatization. Here we investigate the effects of EVs derived from neuroblastoma (NB), a pediatric solid tumor, on metastatic niche formation using the zebrafish as an in vivo model. Intravascular injection in zebrafish embryos allows a non-invasive visualization of EVs dispersion, uptake, and interactions with host cells. To improve repeatability of our results and ease the injection steps, we used an agarose device replica molded from a custom designed micromilled aluminum mold. We first demonstrated that EVs released under hypoxic conditions promote angiogenesis and are more easily internalized by endothelial cells than those purified from normoxic cells. We also showed that injection of with hypoxic EVs increased macrophages mobilization. We then focused on the caudal hematopoietic tissue (CHT) region of the embryo as a potential metastatic site. After hypoxic EVs injection, we highlighted changes in the expression of mmp-9 and cxcl8b genes. Furthermore, we investigated the ability of NB-derived EVs to prime a metastatic niche by a two-step injection of EVs first, followed by NB cells. Interestingly, we found that embryos injected with hypoxic EVs had more proliferating NB cells than those injected with normoxic EVs. Our findings suggest that EVs released by hypoxic NB cells alter the behavior of recipient cells in the zebrafish embryo and promote metastatic outgrowth. In addition, we demonstrated the ability of the zebrafish embryo to be a suitable model for studying the interactions between EVs and recipient cells in the metastatic process.

Protocol for whole-mount preparation, clearing, and visualization of the adult zebrafish spinal cord structures

The vascular repair, a pivotal element of the spinal cord (SC) injury response, has been notably neglected in zebrafish research. Here, we detail the extraction and dissection of whole-mount zebrafish SCs and the optimized whole-mount immunofluorescence staining and clearing protocols for the visualization of SC structures, such as the vascular network. Additional downstream applications of these samples, from gelatin embedding to cryosectioning and tissue staining, can be done after clearing reversion and are also described in this work. For complete details on the use and execution of this protocol, please refer to Ribeiro et al.1.

Diverse Epithelial Lymphocytes in Zebrafish Revealed Using a Novel Scale Biopsy Method

Zebrafish (Danio rerio) are a compelling model for studying lymphocytes because zebrafish and humans have similar adaptive immune systems, including their lymphocytes. Antibodies that recognize zebrafish proteins are sparse, so many investigators use transgenic, lymphocyte-specific fluorophore-labeled lines. Human and zebrafish lymphocyte types are conserved, but many aspects of zebrafish lymphocyte biology remain uninvestigated, including lymphocytes in peripheral tissues, like epidermis. This study is, to our knowledge, the first study to focus on zebrafish epidermal lymphocytes, using scales. Obtaining zebrafish blood via nonlethal methods is difficult; scales represent a source to longitudinally sample live fish. We developed a novel biopsy technique, collecting scales to analyze epithelial lymphocytes from several transgenic lines. We imaged scales via confocal microscopy and demonstrated multiple lymphocyte types in scales/epidermis, quantifying them flow cytometrically. We profiled gene expression of scale, thymic, and kidney-marrow (analogous to mammalian bone marrow) lymphocytes from the same animals, revealing B- and T-lineage signatures. Single-cell quantitative real-time PCR and RNA sequencing show not only canonical B and T cells but also novel lymphocyte populations not described previously. To validate longitudinal scale biopsies, we serially sampled scales from fish treated with dexamethasone, demonstrating epidermal lymphocyte responses. To analyze cells functionally, we employed a bead-ingestion assay, showing that thymic, marrow, and epidermal lymphocytes have phagocytic activity. In summary, we establish a novel, nonlethal technique to obtain zebrafish lymphocytes, providing the first quantification, expression profiling, and functional data from zebrafish epidermal lymphocytes.

Perivascular Macrophages Convert Physical Wound Signals Into Rapid Vascular Responses

Leukocytes detect distant wounds within seconds to minutes, which is essential for effective pathogen defense, tissue healing, and regeneration. Blood vessels must detect distant wounds just as rapidly to initiate local leukocyte extravasation, but the mechanism behind this immediate vascular response remains unclear. Using high-speed imaging of live zebrafish larvae, we investigated how blood vessels achieve rapid wound detection. We monitored two hallmark vascular responses: vessel dilation and serum exudation. Our experiments-including genetic, pharmacologic, and osmotic perturbations, along with chemogenetic leukocyte depletion-revealed that the cPla2 nuclear shape sensing pathway in perivascular macrophages converts a fast (~50 μm/s) osmotic wound signal into a vessel-permeabilizing, 5-lipoxygenase (Alox5a) derived lipid within seconds of injury. These findings demonstrate that perivascular macrophages act as physicochemical relays, bridging osmotic wound signals and vascular responses. By uncovering this novel type of communication, we provide new insights into the coordination of immune and vascular responses to injury.

A dataset of transcriptomic effects of camptothecin treatment on early zebrafish embryos

Zebrafish (Danio rerio) are a good model for cancer research including studies on chemotherapy treatments. We treated wild-type and miR-34a deletion mutant zebrafish embryos at 24 h post-fertilization with 1 µM of the topoisomerase I inhibitor, camptothecin (CPT), for 4 h to catalogue gene expression changes induced by this DNA damage treatment and to understand if these changes are influenced by loss of miR-34a. The 4 sample groups of 3 independent biological samples consisting of 30 embryos each were analyzed by RNA-sequencing using the recently updated zebrafish transcriptome annotation based on GRCz11, which enabled a more complete and sensitive read mapping and gene assignment than standard annotations. Using this gene expression estimates dataset as the primary resource, we performed a differentially expressed gene (DEG) analysis based on treatment as loss of miR-34a had minimal effects on CPT-induced expression changes. The DEGs were analyzed for Gene Ontology and KEGG pathway terms. Enriched terms and pathways among up-regulated genes were mostly related to stress, cell death, cell cycle regulation, transcriptional regulation, cell signalling, developmental processes and synthesis of retinol and steroid hormones. By contrast, down-regulated genes were most strongly associated with genes involved in key developmental processes, adhesion molecules, as well as some transport and metabolic pathways, together suggesting a "developmental shutdown". We also identified interferon-regulated genes and p53 target genes activated or inhibited by DNA damage due to topoisomerase I inhibition, suggesting that they are important components of the response to this type of DNA damage in zebrafish embryos.

The effects of perfluorooctanoic acid on breast cancer metastasis depend on the phenotypes of the cancer cells: An in vivo study with zebrafish xenograft model

Per- and polyfluorinated substances (PFAS) have been associated with numerous human diseases. Recent in vitro studies have implicated the association of PFAS with an increased risk of breast cancer in humans. This study aimed to assess the toxic effects of PFAS during the development of human breast cancer using a zebrafish xenograft model. Perfluorooctanoic acid (PFOA) was used as a PFAS chemical of interest for this study. Two common breast cancer cell lines, MCF-7 and MDA-MB-231, were used to represent the diversity of breast cancer phenotypes. Human preadipocytes were co-implanted with the breast cancer cells into the zebrafish embryos to optimize the microenvironment for tumor cells in vivo. With this modified model, we evaluated the potential effects of the PFOA on the metastatic potential of the two types of breast cancer cells. The presence of human preadipocytes resulted in an enhancement to the metastasis progress of the two types of cells, including the promotion of cell in vivo migration and proliferation, and the increased expression levels of metastatic biomarkers. The enhancement of MCF-7 proliferation by preadipocytes was observed after 2 days post injection (dpi) while the increase of MDA-MB-231 proliferation was seen after 6 dpi. The breast cancer metastatic biomarkers, cadherin 1 (cdh1), and small breast epithelial mucin (sbem) genes demonstrated significant down- and upregulations respectively, by the co-injection of preadipocytes. In the optimized xenograft model, the PFOA consistently promoted cell proliferation and migration and altered the metastatic biomarker expression in MCF-7, which suggested a metastatic effect of PFOA on MCF-7. However, those effects were not consistently observed in MDA-MB-231. The presence of the preadipocytes in the xenograft model may provide a necessary microenvironment for the progress of tumor cells in zebrafish embryos. The finding suggested that the impacts of PFOA exposure on different phenotypes of breast cancers may differ.

Emerging insights in senescence: pathways from preclinical models to therapeutic innovations

Senescence is a crucial hallmark of ageing and a significant contributor to the pathology of age-related disorders. As committee members of the young International Cell Senescence Association (yICSA), we aim to synthesise recent advancements in the identification, characterisation, and therapeutic targeting of senescence for clinical translation. We explore novel molecular techniques that have enhanced our understanding of senescent cell heterogeneity and their roles in tissue regeneration and pathology. Additionally, we delve into in vivo models of senescence, both non-mammalian and mammalian, to highlight tools available for advancing the contextual understanding of in vivo senescence. Furthermore, we discuss innovative diagnostic tools and senotherapeutic approaches, emphasising their potential for clinical application. Future directions of senescence research are explored, underscoring the need for precise, context-specific senescence classification and the integration of advanced technologies such as machine learning, long-read sequencing, and multifunctional senoprobes and senolytics. The dual role of senescence in promoting tissue homoeostasis and contributing to chronic diseases highlights the complexity of targeting these cells for improved clinical outcomes.

Single cell autofluorescence imaging reveals immediate metabolic shifts of neutrophils with activation across biological systems

Neutrophils, the most abundant leukocytes in human peripheral circulation, are crucial for the innate immune response. They are typically quiescent but rapidly activate in response to infection and inflammation, performing diverse functions such as oxidative burst, phagocytosis, and NETosis, which require significant metabolic adaptation. Deeper insights into such metabolic changes will help identify regulation of neutrophil functions in health and diseases. Due to their short lifespan and associated technical challenges, the metabolic processes of neutrophils are not completely understood. This study uses optical metabolic imaging (OMI), which entails optical redox ratio and fluorescence lifetime imaging microscopy of intrinsic metabolic coenzymes NAD(P)H and FAD to assess the metabolic state of single neutrophils. Primary human neutrophils were imaged in vitro under a variety of activation conditions and metabolic pathway inhibitors, while metabolic and functional changes were confirmed with mass spectrometry, oxidative burst, and NETosis measurements. Our findings show that neutrophils undergo rapid metabolic remodeling to a reduced redox state indicated by changes in NAD(P)H lifetime and optical redox ratio, with a shift to an oxidized redox state during activation. Additionally, single cell OMI analysis reveals a heterogeneous metabolic response across neutrophils and human donors to live pathogen infection ( Pseudomonas aeruginosa and Toxoplasma gondii ). Finally, consistent OMI changes with activation were confirmed between in vitro human and in vivo zebrafish larvae neutrophils. This study demonstrates the potential of OMI as a versatile tool for studying neutrophil metabolism and underscores its use across different biological systems, offering insights into neutrophil metabolic activity and function at a single cell level.

Axial muscle-fibre orientations in larval zebrafish

Most teleost fish propel themselves with lateral body waves powered by their axial muscles. These muscles also power suction feeding through rapid expansion of the mouth cavity. They consist of muscle segments (myomeres), separated by connective tissue sheets (myosepts). In adult teleosts, the fast axial muscle fibres follow pseudo-helical trajectories, which are thought to distribute strain (relative fibre length change) approximately evenly across transverse sections during swimming, thereby optimizing power generation. To achieve strain equalization, a significant angle to the longitudinal axis on the frontal plane (azimuth) is necessary near the medial plane, increasing strain. Additionally, a deviation from longitudinal orientation on the sagittal plane (elevation) is required laterally to decrease strain. Despite several detailed morphological studies, our understanding of muscle-fibre orientations in the entire axial musculature of fish remains incomplete. Furthermore, most research has been done in post-larval stages, leaving a knowledge gap regarding the changing axial muscle architecture during larval development. Larval fish exhibit different body size, body shape and swimming kinematics compared to adults. They experience relatively high viscous forces, requiring higher tail-beat amplitudes to overcome increased drag. Additionally, larval fish swim with higher tail-beat frequencies. Histological studies have shown that in larval fish, muscle fibres in the anal region transition from an almost longitudinal orientation to a pseudo-helical pattern by 3 dpf (days post-fertilization). However, these studies were limited to a few sections of the body and were prone to shrinkage and tissue damage. Here, we introduce a novel methodology for quantifying muscle-fibre orientations along the entire axial muscles. We selected 4 dpf larval zebrafish for our analyses, a stage where larvae are actively swimming but not yet free-feeding. High-resolution confocal 3D scans were obtained from four genetically modified zebrafish expressing green fluorescent protein in fast muscle fibres. Fluorescence variation allowed segmentation of individual muscle fibres, which were then converted to fish-bound coordinates by correcting for the fish's position and orientation in the scan, and normalized to pool results across individuals. We show that at 4 dpf, muscle-fibre trajectories exhibit a helical pattern tapering towards the tail. Average fibre angles decrease from anterior to posterior, with azimuth varying over the dorsoventral axis and elevation varying over the mediolateral axis. Notably, only the anteriormost 20% of the body displayed higher azimuth angles near the medial plane. Angles between neighbouring fibres were substantial, particularly at the rim of the epaxial and hypaxial muscles. The revealed muscle-fibre architecture at this age presumably contributes to the swimming performance of these larvae, but that swimming performance is probably not the only driving factor for the fibre pattern. Our methodology offers a promising avenue for exploring muscle-fibre orientations across ontogenetic series and provides a foundation for in-depth functional studies on the role of muscle architecture in facilitating swimming performance of larval fish.

Glutaraldehyde-enhanced autofluorescence as a general tool for 3D morphological imaging

Routine histochemical techniques are capable of producing vast amount of information from diverse sample types, but these techniques are limited in their ability to generate 3D information. Autofluorescence imaging can be used to analyse samples in 3D but it suffers from weak/low signal intensities. Here, we describe a simple chemical treatment with glutaraldehyde to enhance autofluorescence for 3D fluorescence imaging and to generate detailed morphological images on whole-mount samples. This methodology is straightforward and cost-effective to implement, suitable for a wide range of organisms and sample types. Furthermore, it can be readily integrated with standard confocal and fluorescence microscopes for analysis. This approach has the potential to facilitate the analysis of biological 3D structures and research in developmental biology, including studies on model and non-model organisms.

dab2 is required for the scavenging function of lymphatic endothelial cells in the zebrafish meninges

To date it is only partially understood how the brain is cleared of waste products resulting from its high metabolic activity, although this process has important implications for the development and progression of neurodegenerative diseases. Lymphatic vessels play a central role in maintaining fluid and tissue homeostasis, and the recent description of meningeal lymphatic vessels within the dura mater of mice, human and zebrafish has raised considerable interest in unraveling the function of these vessels. In zebrafish, brain lymphatic endothelial cells (BLECs) constitute an additional meningeal lymphatic endothelial cell population. These highly endocytically active cells contribute to the clearance of the brain, but the molecular basis of this scavenging activity is only poorly understood. Here, we report on the characterization of zebrafish disabled 2 (dab2) mutants. Embryos lacking maternally provided dab2 show defective venous sprouting from the caudal vein plexus at 26hpf. Furthermore, we show that the cargo-specific adaptor protein is specifically expressed in BLECs, and that BLECs are significantly impeded in their capacity to internalize specific substrates injected into the cerebrospinal fluid upon loss of zygotic dab2. Our work therefore identifies Dab2 as an important member of the molecular machinery mediating the scavenging function of BLECs in the meninges.

Structure and Topography of Facial Branchiomotor Neuron Dendrites in Larval Zebrafish (Danio rerio)

Motor circuits in the vertebrate hindbrain need to become functional early in development. What are the fundamental mechanisms that establish early synaptic inputs to motor neurons? Previous evidence is consistent with the hypothesis that motor neuron dendrite positioning serves a causal role in early spinal motor circuit development, with initial connectivity determined by the overlap between premotor axons and motor neuron dendrites (perhaps without the need for molecular recognition). Does motor neuron dendrite topography serve a similar role in the hindbrain? In the current study, we provide the first quantitative analysis of the dendrites of facial branchiomotor neurons (FBMNs) in larval zebrafish. We previously demonstrated that FBMNs exhibit functional topography along the dorsoventral axis, with the most ventral cell bodies most likely to exhibit early rhythmic activity-suggesting that FBMNs with ventral cell bodies are most likely to receive inputs from premotor neurons carrying rhythmic respiratory signals. We hypothesized that this functional topography can be explained by differences in dendrite positioning, giving ventral FBMNs preferential access to premotor axons carrying rhythmic signals. If this hypothesis is true, we predicted that FBMN cell body position would be correlated with dendrite position along the dorsoventral axis. To test this prediction, we used single-cell labeling to trace the dendritic arbors of FBMNs in larval zebrafish at 5-days post-fertilization (dpf). FBMN dendrites varied in complexity, and this variation could not be attributed to differences in the relative age of neurons. Most dendrites grew caudally, laterally, and ventrally from the cell body-though FBMN dendrites could extend their dendrites dorsally. Across our sample, FBMN cell body position correlated with dendrite position along the dorsoventral axis, consistent with our hypothesis that differences in dendrite positioning serve as the substrate for differences in activity patterns across neurons. Future studies will build on this foundational data, testing additional predictions of the central hypothesis-to further investigate the mechanisms of early motor circuit development.

Primary Bone Tumors and Breast Cancer-Induced Bone Metastases: In Vivo Animal Models and New Alternative Approaches

Bone is the preferential site of metastasis for the most common tumors, including breast cancer. On the other hand, osteosarcoma is the primary bone cancer that most commonly occurs and causes bone cancer-related deaths in children. Several treatment strategies have been developed so far, with little or no efficacy for patient survival and with the development of side effects. Therefore, there is an urgent need to develop more effective therapies for bone primary tumors and bone metastatic disease. This almost necessarily requires the use of in vivo animal models that better mimic human pathology and at the same time follow the ethical principles for the humane use of animal testing. In this review we aim to illustrate the main and more suitable in vivo strategies employed to model bone metastases and osteosarcoma. We will also take a look at the recent technologies implemented for a partial replacement of animal testing.

Mimicking and analyzing the tumor microenvironment

The tumor microenvironment (TME) is increasingly appreciated to play a decisive role in cancer development and response to therapy in all solid tumors. Hypoxia, acidosis, high interstitial pressure, nutrient-poor conditions, and high cellular heterogeneity of the TME arise from interactions between cancer cells and their environment. These properties, in turn, play key roles in the aggressiveness and therapy resistance of the disease, through complex reciprocal interactions between the cancer cell genotype and phenotype, and the physicochemical and cellular environment. Understanding this complexity requires the combination of sophisticated cancer models and high-resolution analysis tools. Models must allow both control and analysis of cellular and acellular TME properties, and analyses must be able to capture the complexity at high depth and spatial resolution. Here, we review the advantages and limitations of key models and methods in order to guide further TME research and outline future challenges.

Loss of Dnajc21 leads to cytopenia and altered nucleotide metabolism in zebrafish

Mutations in the DNAJC21 gene were recently described in Shwachman-Diamond syndrome (SDS), a bone marrow failure syndrome with high predisposition for myeloid malignancies. To study the underlying biology in hematopoiesis regulation and disease, we generated the first in vivo model of Dnajc21 deficiency using the zebrafish. Zebrafish dnajc21 mutants phenocopy key SDS patient phenotypes such as cytopenia, reduced growth, and defective protein synthesis. We show that cytopenia results from impaired hematopoietic differentiation, accumulation of DNA damage, and reduced cell proliferation. The introduction of a biallelic tp53 mutation in the dnajc21 mutants leads to the development of myelodysplastic neoplasia-like features defined by abnormal erythroid morphology and expansion of hematopoietic progenitors. Using transcriptomic and metabolomic analyses, we uncover a novel role for Dnajc21 in nucleotide metabolism. Exogenous nucleoside supplementation restores neutrophil counts, revealing an association between nucleotide imbalance and neutrophil differentiation, suggesting a novel mechanism in dnajc21-mutant SDS biology.

Comparative insight into the regenerative mechanisms of the adult brain in zebrafish and mouse: highlighting the importance of the immune system and inflammation in successful regeneration

Regeneration, the complex process of restoring damaged or absent cells, tissues, and organs, varies considerably between species. The zebrafish is a remarkable model organism for its impressive regenerative abilities, particularly in organs such as the heart, fin, retina, spinal cord, and brain. Unlike mammals, zebrafish can regenerate with limited or absent scarring, a phenomenon closely linked to the activation of stem cells and immune cells. This review examines the unique roles played by the immune response and inflammation in zebrafish and mouse during regeneration, highlighting the cellular and molecular mechanisms behind their divergent regenerative capacities. By focusing on zebrafish telencephalic regeneration and comparing it to that of the rodents, this review highlights the importance of a well-controlled, acute, and non-persistent immune response in zebrafish, which promotes an environment conducive to regeneration. The knowledge gained from understanding the mechanisms of zebrafish regeneration holds great promises for the treatment of human neurodegenerative diseases and brain damage (stroke and traumatic brain injuries), as well as for the advancement of regenerative medicine approaches.

Impact of the Graphene Production Methods Sonication and Microfluidization on In Vitro and In Vivo Toxicity, Macrophage Response, and Complement Activation

Graphene, a material composed of a two-dimensional lattice of carbon atoms, has due to its many unique properties a wide array of potential applications in the biomedical field. One of the most common production methods is exfoliation through sonication, which is simple but has low yields. Another approach, using microfluidization, has shown promise through its scalability for commercial production. Regardless of their production method, materials made for biomedical applications need to be tested for biocompatibility. Here, we investigated the differences in toxicity, macrophage response, and complement activation of similar-sized graphene flakes produced through sonication and microfluidization, using in vitro cell assays and in vivo assays on zebrafish larvae. In vitro toxicity testing showed that sonicated graphene had a high toxicity, with an EC50 of 100 μg mL-1 for endothelial cells and 60 μg mL-1 for carcinoma cells. In contrast, microfluidized graphene did not reach EC50 at any of the tested concentrations. The potency to activate the complement system in whole blood was 10-fold higher for sonicated than for microfluidized graphene. In zebrafish larvae, graphene of either production method was found to mainly agglomerate in the caudal hematopoietic tissue; however, no acute toxic effects were found. Sonicated graphene led to an increase in macrophage count and a macrophage migration to the ventral tail area, while microfluidized graphene led to a transient reduction in macrophage count and fewer cells in the ventral trail area. The observed reduction in macrophages and change in macrophage distribution following exposure to microfluidized graphene was less pronounced compared to sonicated graphene and contributed to masking of the fluorescent signal rather than cytotoxic effects. Summarized, we observed higher toxicity, macrophage response, and complement activation with graphene produced through sonication, which could be due to oxygen-containing functional groups introduced to the edge of the carbon lattice by this production method. These findings indicate that microfluidization produces graphene more suitable for biomedical applications.

Stripe pattern differences can be used to distinguish individual adult zebrafish

Adult zebrafish are commonly used as disease models in biomedical research, but unlike in other model organisms such as rodents, there is no simple method for distinguishing individuals, even though the importance of individual differences is recognized in such research. We developed a side viewing device that can be used to capture images of stripe patterns and identified eight distinct components of stripe patterns on the caudal and anal fins that allowed us to distinguish individual fish. We found that the stripe patterns were consistent for at least 8 weeks in males and females of two lines of wild-type zebrafish. These results suggest that individual adult zebrafish can be distinguished in an easy and non-invasive manner, allowing researchers to incorporate individual differences in biomedical research as in rodent models.

Craters on the melanoma surface facilitate tumor-immune interactions and demonstrate pathologic response to checkpoint blockade in humans

Immunotherapy leads to cancer eradication despite the tumor's immunosuppressive environment. Here, we used extended long-term in-vivo imaging and high-resolution spatial transcriptomics of endogenous melanoma in zebrafish, and multiplex imaging of human melanoma, to identify domains that facilitate immune response during immunotherapy. We identified crater-shaped pockets at the margins of zebrafish and human melanoma, rich with beta-2 microglobulin (B2M) and antigen recognition molecules. The craters harbor the highest density of CD8+ T cells in the tumor. In zebrafish, CD8+ T cells formed prolonged interactions with melanoma cells within craters, characteristic of antigen recognition. Following immunostimulatory treatment, the craters enlarged and became the major site of activated CD8+ T cell accumulation and tumor killing that was B2M dependent. In humans, craters predicted immune response to ICB therapy, showing response better than high T cell infiltration. This marks craters as potential new diagnostic tool for immunotherapy success and targets to enhance ICB response.

Transcripts of repetitive DNA elements signal to block phagocytosis of hematopoietic stem cells

Macrophages maintain hematopoietic stem cell (HSC) quality by assessing cell surface Calreticulin (Calr), an "eat-me" signal induced by reactive oxygen species (ROS). Using zebrafish genetics, we identified Beta-2-microglobulin (B2m) as a crucial "don't eat-me" signal on blood stem cells. A chemical screen revealed inducers of surface Calr that promoted HSC proliferation without triggering ROS or macrophage clearance. Whole-genome CRISPR-Cas9 screening showed that Toll-like receptor 3 (Tlr3) signaling regulated b2m expression. Targeting b2m or tlr3 reduced the HSC clonality. Elevated B2m levels correlated with high expression of repetitive element (RE) transcripts. Overall, our data suggest that RE-associated double-stranded RNA could interact with TLR3 to stimulate surface expression of B2m on hematopoietic stem and progenitor cells. These findings suggest that the balance of Calr and B2m regulates macrophage-HSC interactions and defines hematopoietic clonality.

Seminar: Functional Exposomics and Mechanisms of Toxicity-Insights from Model Systems and NAMs

BACKGROUND

Significant progress has been made over the past decade in measuring the chemical components of the exposome, providing transformative population-scale frameworks in probing the etiologic link between environmental factors and disease phenotypes. While the analytical technologies continue to evolve with reams of data being generated, there is an opportunity to complement exposome-wide association studies (ExWAS) with functional analyses to advance etiologic search at organismal, cellular, and molecular levels.

OBJECTIVES

Exposomics is a transdisciplinary field aimed at enabling discovery-based analysis of the nongenetic factors that contribute to disease, including numerous environmental chemical stressors. While advances in exposure assessment are enhancing population-based discovery of exposome-wide effects and chemical exposure agents, functional screening and elucidation of biological effects of exposures represent the next logical step toward precision environmental health and medicine. In this work, we focus on the use, strategies, and prospects of alternative approaches and model systems to enhance the current human exposomics framework in biomarker search and causal understanding, spanning from bench-based nonmammalian organisms and cell culture to computational new approach methods (NAMs).

DISCUSSION

We visit the definition of the functional exposome and exposomics and discuss a need to leverage alternative models as opposed to mammalian animals for delineating exposome-wide health effects. Under the "three Rs" principle of reduction, replacement, and refinement, model systems such as roundworms, fruit flies, zebrafish, and induced pluripotent stem cells (iPSCs) are advantageous over mammals (e.g., rodents or higher vertebrates). These models are cost-effective, and cell-specific genetic manipulations in these models are easier and faster, compared to mammalian models. Meanwhile, in silico NAMs enhance hazard identification and risk assessment in humans by bridging the translational gaps between toxicology data and etiologic inference, as represented by in vitro to in vivo extrapolation (IVIVE) and integrated approaches to testing and assessment (IATA) under the adverse outcome pathway (AOP) framework. Together, these alternatives offer a strong toolbox to support functional exposomics to study toxicity and causal mediators underpinning exposure-disease links. https://doi.org/10.1289/EHP13120.

Metabolic disrupting chemicals in the intestine: the need for biologically relevant models: Zebrafish: what can we learn from this small environment-sensitive fish?

Although the concept of endocrine disruptors first appeared almost 30 years ago, the relatively recent involvement of these substances in the etiology of metabolic pathologies (obesity, diabetes, hepatic steatosis, etc.) has given rise to the concept of Metabolic Disrupting Chemicals (MDCs). Organs such as the liver and adipose tissue have been well studied in the context of metabolic disruption by these substances. The intestine, however, has been relatively unexplored despite its close link with these organs. In vivo models are useful for the study of the effects of MDCs in the intestine and, in addition, allow investigations into interactions with the rest of the organism. In the latter respect, the zebrafish is an animal model which is used increasingly for the characterization of endocrine disruptors and its use as a model for assessing effects on the intestine will, no doubt, expand. This review aims to highlight the importance of the intestine in metabolism and present the zebrafish as a relevant alternative model for investigating the effect of pollutants in the intestine by focusing, in particular, on cytochrome P450 3A (CYP3A), one of the major molecular players in endogenous and MDCs metabolism in the gut.

The Role of the Neurotrophin Network in Skin Squamous Cell Cancer and the Novel Use of the Zebrafish System

Cutaneous squamous cell carcinoma (cSCC) is the second most prevalent form of skin cancer. An increasing number of cSCCs are associated with dysregulation of key molecules that control skin homeostasis. These observations have increased interest in the role of neurotrophins and their receptors in the pathogenesis of cSCC. They have been demonstrated to have a considerable impact on the aggressiveness potential of skin cancer by both in vitro and in vivo models. In this context, mouse models are classically used to dissect proliferation versus differentiation balance, but they have some limitations in terms of time, space, and costs. Recently, zebrafish models have been implemented as a new tool to obtain information regarding the invasive capacity and metastasis of neoplastic cells. By xenotransplantation technique, cSCC cells from a patient's biopsy or cell line can be successfully characterized, with or without the presence of genetic manipulation or treatments. In addition, the evaluation of the immune microenvironment contributes to potentially identifying connections and homologies with humans. In this review, we retrace the role of the neurotrophin network in healthy and pathological skin, particularly in cSCC. We review how zebrafish models can be important tools for studying cSCC development, growth, and potential treatments.

Staphylococcus aureus lipid factors modulate melanoma cell clustering and invasion

The microbiome can influence cancer development and progression. However, less is known about the role of the skin microbiota in melanoma. Here, we took advantage of a zebrafish melanoma model to probe the effects of Staphylococcus aureus on melanoma invasion. We found that S. aureus produces factors that enhance melanoma invasion and dissemination in zebrafish larvae. We used a published in vitro 3D cluster formation assay that correlates increased clustering with tumor invasion. S. aureus supernatant increased clustering of melanoma cells and was abrogated by a Rho-Kinase inhibitor, implicating a role for Rho-GTPases. The melanoma clustering response was specific to S. aureus but not to other staphylococcal species, including S. epidermidis. Our findings suggest that S. aureus promotes melanoma clustering and invasion via lipids generated by the lipase Sal2 (officially known as GehB). Taken together, these findings suggest that specific bacterial products mediate melanoma invasive migration in zebrafish.

In vivo monitoring of leukemia-niche interactions in a zebrafish xenograft model

Acute lymphoblastic leukemia (ALL) is the most common type of malignancy in children. ALL prognosis after initial diagnosis is generally good; however, patients suffering from relapse have a poor outcome. The tumor microenvironment is recognized as an important contributor to relapse, yet the cell-cell interactions involved are complex and difficult to study in traditional experimental models. In the present study, we established an innovative larval zebrafish xenotransplantation model, that allows the analysis of leukemic cells (LCs) within an orthotopic niche using time-lapse microscopic and flow cytometric approaches. LCs homed, engrafted and proliferated within the hematopoietic niche at the time of transplant, the caudal hematopoietic tissue (CHT). A specific dissemination pattern of LCs within the CHT was recorded, as they extravasated over time and formed clusters close to the dorsal aorta. Interactions of LCs with macrophages and endothelial cells could be quantitatively characterized. This zebrafish model will allow the quantitative analysis of LCs in a functional and complex microenvironment, to study mechanisms of niche mediated leukemogenesis, leukemia maintenance and relapse development.

Peds1 deficiency in zebrafish results in myeloid cell apoptosis and exacerbated inflammation

Plasmalogens are glycerophospholipids with a vinyl ether bond that confers unique properties. Recent identification of the gene encoding PEDS1, the desaturase generating the vinyl ether bond, enables evaluation of the role of plasmalogens in health and disease. Here, we report that Peds1-deficient zebrafish larvae display delayed development, increased basal inflammation, normal hematopoietic stem and progenitor cell emergence, and cell-autonomous myeloid cell apoptosis. In a sterile acute inflammation model, Peds1-deficient larvae exhibited impaired inflammation resolution and tissue regeneration, increased interleukin-1β and NF-κB expression, and elevated ROS levels at the wound site. Abnormal immune cell recruitment, neutrophil persistence, and fewer but predominantly pro-inflammatory macrophages were observed. Chronic skin inflammation worsened in Peds1-deficient larvae but was mitigated by exogenous plasmalogen, which also alleviated hyper-susceptibility to bacterial infection, as did pharmacological inhibition of caspase-3 and colony-stimulating factor 3-induced myelopoiesis. Overall, our results highlight an important role for plasmalogens in myeloid cell biology and inflammation.

Inhibition of GPR68 kills glioblastoma in zebrafish xenograft models

OBJECTIVE

Inhibition and knockdown of GPR68 negatively affects glioblastoma cell survival in vitro by inducing ferroptosis. Herein, we aimed to demonstrate that inhibition of GPR68 reduces the survival of glioblastoma cells in vivo using two orthotopic larval xenograft models in Danio rerio, using GBM cell lines U87-MG and U138-MG. In vivo survival of the cancer cells was assessed in the setting of GPR68 inhibition or knockdown.

RESULTS

In vitro, shRNA-mediated knockdown of GPR68 inhibition demonstrated potent cytotoxic effects against U87 and U138 glioblastoma cell lines. This effect was associated with increased intracellular lipid peroxidation, suggesting ferroptosis as the underlying mechanism of cell death. Translating these findings in vivo, we established a novel xenograft model in zebrafish by successfully grafting fluorescently labeled human glioblastoma cells, which were previously shown to overexpress GPR68. shRNA knockdown of GPR68 significantly reduced the viability of grafted GBM cells within this model. Additionally, treatment with ogremorphin (OGM), a highly specific small molecule inhibitor of GPR68, also reduced the viability of grafted GBM cells with limited toxicity to the developing zebrafish embryos. This study suggests that therapeutic targeting of GPR68 with small molecules like OGM represents a promising approach for the treatment of GBM.

Restraint of melanoma progression by cells in the local skin environment

Keratinocytes, the dominant cell type in the melanoma microenvironment during tumor initiation, exhibit diverse effects on melanoma progression. Using a zebrafish model of melanoma and human cell co-cultures, we observed that keratinocytes undergo an Epithelial-Mesenchymal Transition (EMT)-like transformation in the presence of melanoma, reminiscent of their behavior during wound healing. Surprisingly, overexpression of the EMT transcription factor Twist in keratinocytes led to improved overall survival in zebrafish melanoma models, despite no change in tumor initiation rates. This survival benefit was attributed to reduced melanoma invasion, as confirmed by human cell co-culture assays. Single-cell RNA-sequencing revealed a unique melanoma cell cluster in the Twist-overexpressing condition, exhibiting a more differentiated, less invasive phenotype. Further analysis nominated homotypic jam3b-jam3b and pgrn-sort1a interactions between Twist-overexpressing keratinocytes and melanoma cells as potential mediators of the invasive restraint. Our findings suggest that EMT in the tumor microenvironment (TME) may limit melanoma invasion through altered cell-cell interactions.

Live imaging in zebrafish reveals tissue-specific strategies for amoeboid migration

Amoeboid cells like leukocytes can enter and migrate within virtually every tissue of the body, even though tissues vary widely in their chemical and mechanical composition. Here, we imaged motile T cells as they colonized peripheral tissues during zebrafish development to ask if cells tailor their migration strategy to their local tissue environment. We found that T cells in most sites migrated with f-actin-rich leading-edge pseudopods, matching how they migrate in vitro . T cells notably deviated from this strategy in the epidermis, where they instead migrated using a rearward concentration of f-actin and stable leading-edge blebs. This mode of migration occurs under planar confinement in vitro , and we correspondingly found the stratified keratinocyte layers of the epidermis impose planar-like confinement on leukocytes in vivo . By imaging the same cell type across the body, our data collectively indicates that cells adapt their migration strategy to navigate different tissue geometries in vivo .

Reprogramming macrophages with R848-loaded artificial protocells to modulate skin and skeletal wound healing

After tissue injury, inflammatory cells are rapidly recruited to the wound where they clear microbes and other debris, and coordinate the behaviour of other cell lineages at the repair site in both positive and negative ways. In this study, we take advantage of the translucency and genetic tractability of zebrafish to evaluate the feasibility of reprogramming innate immune cells in vivo with cargo-loaded protocells and investigate how this alters the inflammatory response in the context of skin and skeletal repair. Using live imaging, we show that protocells loaded with R848 cargo (which targets TLR7 and TLR8 signalling), are engulfed by macrophages resulting in their switching to a pro-inflammatory phenotype and altering their regulation of angiogenesis, collagen deposition and re-epithelialization during skin wound healing, as well as dampening osteoblast and osteoclast recruitment and bone mineralization during fracture repair. For infected skin wounds, R848-reprogrammed macrophages exhibited enhanced bactericidal activities leading to improved healing. We replicated our zebrafish studies in cultured human macrophages, and showed that R848-loaded protocells similarly reprogramme human cells, indicating how this strategy might be used to modulate wound inflammation in the clinic.