Intelectin 3 is dispensable for resistance against a mycobacterial infection in zebrafish (Danio rerio)

Therapeutic Nonsense Suppression Modalities: From Small Molecules to Nucleic Acid-Based Approaches

Nonsense mutations are genetic mutations that create premature termination codons (PTCs), leading to truncated, defective proteins in diseases such as cystic fibrosis, neurofibromatosis type 1, Dravet syndrome, Hurler syndrome, Beta thalassemia, inherited bone marrow failure syndromes, Duchenne muscular dystrophy, and even cancer. These mutations can also trigger a cellular surveillance mechanism known as nonsense-mediated mRNA decay (NMD) that degrades the PTC-containing mRNA. The activation of NMD can attenuate the consequences of truncated, defective, and potentially toxic proteins in the cell. Since approximately 20% of all single-point mutations are disease-causing nonsense mutations, it is not surprising that this field has received significant attention, resulting in a remarkable advancement in recent years. In fact, since our last review on this topic, new examples of nonsense suppression approaches have been reported, namely new ways of promoting the translational readthrough of PTCs or inhibiting the NMD pathway. With this review, we update the state-of-the-art technologies in nonsense suppression, focusing on novel modalities with therapeutic potential, such as small molecules (readthrough agents, NMD inhibitors, and molecular glue degraders); antisense oligonucleotides; tRNA suppressors; ADAR-mediated RNA editing; targeted pseudouridylation; and gene/base editing. While these various modalities have significantly advanced in their development stage since our last review, each has advantages (e.g., ease of delivery and specificity) and disadvantages (manufacturing complexity and off-target effect potential), which we discuss here.

In Search of a Target Gene for a Desirable Phenotype in Aquaculture: Genome Editing of Cyprinidae and Salmonidae Species

Aquaculture supplies the world food market with a significant amount of valuable protein. Highly productive aquaculture fishes can be derived by utilizing genome-editing methods, and the main problem is to choose a target gene to obtain the desirable phenotype. This paper presents a review of the studies of genome editing for genes controlling body development, growth, pigmentation and sex determination in five key aquaculture Salmonidae and Cyprinidae species, such as rainbow trout (Onchorhynchus mykiss), Atlantic salmon (Salmo salar), common carp (Cyprinus carpio), goldfish (Carassius auratus), Gibel carp (Carassius gibelio) and the model fish zebrafish (Danio rerio). Among the genes studied, the most applicable for aquaculture are mstnba, pomc, and acvr2, the knockout of which leads to enhanced muscle growth; runx2b, mutants of which do not form bones in myoseptae; lepr, whose lack of function makes fish fast-growing; fads2, Δ6abc/5Mt, and Δ6bcMt, affecting the composition of fatty acids in fish meat; dnd mettl3, and wnt4a, mutants of which are sterile; and disease-susceptibility genes prmt7, gab3, gcJAM-A, and cxcr3.2. Schemes for obtaining common carp populations consisting of only large females are promising for use in aquaculture. The immobilized and uncolored zebrafish line is of interest for laboratory use.

Innate immune and chronic heat stress responses in sturgeons: Advances and insights from studies on Russian sturgeons

Chronic stress deteriorates the immune function of fish, thereby increasing their vulnerability to infections. However, the molecular and cellular mechanisms underlying stress-mediated immunosuppression and infection susceptibility in fish remain largely unknown. Understanding these mechanisms will contribute to improving fish welfare and their farm production. Herein, we review the challenges of sturgeon aquaculture in subtropical countries, where current climate change has giving rise to significant temperature increments during summer. This leads to the exposure of fish to stressful conditions during these months. Chronic heat stress deserves attention considering the rapid warming rate of the planet. It is already affecting wild fish populations, with disastrous consequences for sturgeons, which are one of the most endangered fish species in the world. In this context, we discuss the most recent advances through the studies on the effects of chronic heat stress on the innate immune components of sturgeons. To this end, we summarise the findings of studies focusing on the aquaculture of Russian sturgeons and observations made on other Acipenser species. Special attention is given to acute-phase proteins, as they might be valuable biomarkers of heat stress and infection, with applicability in monitoring the fish health status in farms.

Characterization of the innate immune response to Streptococcus pneumoniae infection in zebrafish

Streptococcus pneumoniae (pneumococcus) is one of the most frequent causes of pneumonia, sepsis and meningitis in humans, and an important cause of mortality among children and the elderly. We have previously reported the suitability of the zebrafish (Danio rerio) larval model for the study of the host-pathogen interactions in pneumococcal infection. In the present study, we characterized the zebrafish innate immune response to pneumococcus in detail through a whole-genome level transcriptome analysis and revealed a well-conserved response to this human pathogen in challenged larvae. In addition, to gain understanding of the genetic factors associated with the increased risk for severe pneumococcal infection in humans, we carried out a medium-scale forward genetic screen in zebrafish. In the screen, we identified a mutant fish line which showed compromised resistance to pneumococcus in the septic larval infection model. The transcriptome analysis of the mutant zebrafish larvae revealed deficient expression of a gene homologous for human C-reactive protein (CRP). Furthermore, knockout of one of the six zebrafish crp genes by CRISPR-Cas9 mutagenesis predisposed zebrafish larvae to a more severe pneumococcal infection, and the phenotype was further augmented by concomitant knockdown of a gene for another Crp isoform. This suggests a conserved function of C-reactive protein in anti-pneumococcal immunity in zebrafish. Altogether, this study highlights the similarity of the host response to pneumococcus in zebrafish and humans, gives evidence of the conserved role of C-reactive protein in the defense against pneumococcus, and suggests novel host genes associated with pneumococcal infection.

Mycobacteriosis in an appearantly healty atlantic mackerel (Scomber Scombrus, L.) and zoonotic potential

ABSTRACT Mycobacteriosis was detected in seven out of one Atlantic mackerel (Scomber scombrus) that was purchased for human consumption from a fish market. The fish was apparently healthy but during cleaning, several granulomatous foci were noticed in the visceral organs. Histopathological examination of the lesions revealed numerous foci characterized by caseous necrosis in the center of the lesion surrounded by epithelioid giant cells. Ziehl-Neelsen staining revealed the presence of rod-shaped, acid-fast bacteria. Furthermore, immunohistochemical examination revealed the presence of a protein of mycobacterial origin in giant cells and macrophages. Based on gross and microscopic findings, mycobacteriosis was diagnosed. This report showed that due to its zoonotic potential, mycobacteriosis should be considered even in healthy-appearing fishes for human consumption.

Molecular properties and ligand specificity of zebrafish intelectin-2

Intelectins are immune lectins expressed in chordates, including several fish species, in which intelectins are known to be upregulated upon infection. However, the basic biochemical properties and bacteria binding specificities of several fish intelectins are not well studied. We focus our investigation on zebrafish intelectin-2 (DrIntL-2) that is predominantly expressed in the gastrointestinal tract. The disulfide-linked oligomeric state and the cysteine responsible for intermolecular disulfide bonds are identified. DrIntL-2 is a globular particle of around 30 nm. In addition to the typical exocyclic 1,2-diol ligands, DrIntL-2 binds β-1,3-glucan and recognizes Salmonella typhimurium and Pseudomonas aeruginosa. This investigation not only shed light on the fish innate immunity that will be essential for the aquaculture industry, but will also provide a foundation for further application of DrIntL-2 in bacteria detection and identification.

Proprotein convertase subtilisin/kexin type 9 regulates the production of acute-phase reactants from the liver

BACKGROUND & AIMS

Proprotein convertase subtilisin/kexin type 9 (PCSK9) controls blood cholesterol levels by fostering the LDL receptor (LDLR) degradation in hepatocytes. Additionally, PCSK9 has been suggested to participate in immunoregulation by modulating cytokine production. We studied the immunological role of PCSK9 in Streptococcus pneumoniae bacteraemia in vivo and in a human hepatocyte cell line.

METHODS

CRISPR/Cas9 mutagenesis was utilized to create pcsk9 knock-out (KO) zebrafish, which were infected with S pneumoniae to assess the role of PCSK9 for the survival of the fish and in the transcriptomic response of the liver. The direct effects of PCSK9 on the expression of acute-phase reaction (APR) genes were studied in HepG2 cells.

RESULTS

The pcsk9 KO zebrafish lines (pcsk9^tpu-13 and pcsk9^tpu-2,+15 ) did not show developmental defects or gross phenotypical differences. In the S pneumoniae infected zebrafish, the mortality of pcsk9 KOs was similar to the controls. A liver-specific gene expression analysis revealed that a pneumococcal challenge upregulated pcsk9, and that the pcsk9 deletion reduced the expression of APR genes, including hepcidin antimicrobial peptide (hamp) and complement component 7b (c7b). Accordingly, silencing PCSK9 in vitro in HepG2 cells using small interfering RNAs (siRNAs) decreased HAMP expression.

CONCLUSIONS

We demonstrate that PCSK9 is not critical for zebrafish survival in a systemic pneumococcal infection. However, PCSK9 deficiency was associated with the lower expression of APR genes in zebrafish and altered the expression of innate immunity genes in a human hepatocyte cell line. Overall, our data suggest an evolutionarily conserved function for PCSK9 in APR in the liver.

Characterization of a common carp intelectin gene with bacterial binding and agglutination activity

Intelectin (ITLN) is a type of glycan-binding lectin involved in many physiological processes and some human diseases. Here we report a common carp intelectin (cITLN). Like other orthologs, cITLN also contains a conserved fibrinogen-related domain (FReD) and a unique intelectin domain, expresses in all the tissues tested with the highest level in the hindgut, and responds to bacterial challenge in the acute phase. We also expressed cITLN in Escherichia coli (E. coli) system, and the purified recombinant cITLN could neither affect the surface of bacteria nor inhibit the growth of bacteria, but it can agglutinate both gram-positive and gram-negative bacteria in a calcium-dependent manner. The cITLN's ability of agglutination of gram-positive bacteria is stronger than that of gram-negative bacteria. This is probably because recombinant cITLN could binding peptidoglycan (PGN) with a higher degree to lipopolysaccharide (LPS). Our results of cITLN provided new insight into the function of intelectin in the intestinal mucosal immunity.

Serum amyloid A is a positive acute phase protein in Russian sturgeon challenged with Aeromonas hydrophila

The immune system of sturgeons, one of the most ancient and economically valuable fish worldwide, is poorly understood. The lack of molecular tools and data about infection biomarkers hinders the possibility to monitor sturgeon health during farming and detect infection outbreaks. To tackle this issue, we mined publicly available transcriptomic datasets and identified putative positive acute-phase proteins (APPs) of Russian sturgeons that could be induced by a bacterial infection and monitored using non-invasive methods. Teleost literature compelled us to focus on five promising candidates: hepcidin, a warm acclimation associated hemopexin, intelectin, serum amyloid A protein (SAA) and serotransferrin. Among them, SAA was the most upregulated protein at the mRNA level in the liver of sturgeons challenged with heat-inactivated or live Aeromonas hydrophila. To assess whether this upregulation yielded increasing SAA levels in circulation, we developed an in-house ELISA to quantify SAA levels in sturgeon serum. Circulating SAA rose upon bacterial challenge and positively correlated with hepatic saa expression. This is the first time serum SAA has been quantified in an Actinopterygii fish. Since APPs vary across different fish species, our work sheds light on sturgeon acute-phase response, revealing that SAA is a positive APP with potential value as infection biomarker.

Integrating fish models in tuberculosis vaccine development

Tuberculosis is a chronic infection by Mycobacterium tuberculosis that results in over 1.5 million deaths worldwide each year. Currently, there is only one vaccine against tuberculosis, the Bacillus Calmette–Guérin (BCG) vaccine. Despite widespread vaccination programmes, over 10 million new M. tuberculosis infections are diagnosed yearly, with almost half a million cases caused by antibiotic-resistant strains. Novel vaccination strategies concentrate mainly on replacing BCG or boosting its efficacy and depend on animal models that accurately recapitulate the human disease. However, efforts to produce new vaccines against an M. tuberculosis infection have encountered several challenges, including the complexity of M. tuberculosis pathogenesis and limited knowledge of the protective immune responses. The preclinical evaluation of novel tuberculosis vaccine candidates is also hampered by the lack of an appropriate animal model that could accurately predict the protective effect of vaccines in humans. Here, we review the role of zebrafish (Danio rerio) and other fish models in the development of novel vaccines against tuberculosis and discuss how these models complement the more traditional mammalian models of tuberculosis.

Summary: In this Review, we discuss how zebrafish (Danio rerio) and other fish models can complement the more traditional mammalian models in the development of novel vaccines against tuberculosis.

DNA vaccination with the Mycobacterium marinum MMAR_4110 antigen inhibits reactivation of a latent mycobacterial infection in the adult Zebrafish

BACKGROUND

Tuberculosis is a major challenge for health care, as options for its treatment and prevention are limited. Therefore, novel approaches, such as DNA vaccination, to both prevent primary infections and the reactivation of latent infections need to be developed. A Mycobacterium marinum infection in adult zebrafish (Danio rerio) recapitulates features of the human Mycobacterium tuberculosis infection, providing a convenient preclinical animal model for studying tuberculosis.

METHODS

Hypoxic M. marinum cultures were produced with the Wayne model, and further reaerated to replicate the in vivo reactivation in vitro. Expression levels of M. marinum genes were studied with mRNA sequencing from exponentially growing bacteria, anaerobic cultures and at 2 and 12 h after reaeration. Seven reactivation-associated genes were selected for further studies, where their antigen potentiality as DNA-vaccines to prevent reactivation of a latent mycobacterial infection was investigated in the adult zebrafish model. The Mann-Whitney test was used to evaluate differences in bacterial counts between the groups.

RESULTS

The mRNA sequencing data showed that, seven M. marinum genes, MMAR_0444, MMAR_0514, MMAR_0552, MMAR_0641, MMAR_1093, MMAR_4110 and MMAR_4524, were upregulated during reactivation when compared to both dormant and logarithmic growing bacteria. Four different MMAR_4110 antigens prevented the reactivation of a latent mycobacterial infection in the adult zebrafish.

CONCLUSION

This study provides novel information about reactivation-related M. marinum genes. One of the antigens, MMAR_4110, inhibited the reactivation of a latent M. marinum infection in zebrafish, implicating that the characterized genes could be potential targets for further vaccine and drug development against mycobacterial diseases.

Characterization of immune response against Mycobacterium marinum infection in the main hematopoietic organ of adult zebrafish (Danio rerio)

Tuberculosis remains a major global health challenge. To gain information about genes important for defense against tuberculosis, we used a well-established tuberculosis model; Mycobacterium marinum infection in adult zebrafish. To characterize the immunological response to mycobacterial infection at 14 days post infection, we performed a whole-genome level transcriptome analysis using cells from kidney, the main hematopoietic organ of adult zebrafish. Among the upregulated genes, those associated with immune signaling and regulation formed the largest category, whereas the largest group of downregulated genes had a metabolic role. We also performed a forward genetic screen in adult zebrafish and identified a fish line with severely impaired survival during chronic mycobacterial infection. Based on transcriptome analysis, these fish have decreased expression of several immunological genes. Taken together, these results give new information about the genes involved in the defense against mycobacterial infection in zebrafish.