Molecular Actors of Inflammation and Their Signaling Pathways: Mechanistic Insights from Zebrafish

Inflammation is a hallmark of the physiological response to aggressions. It is orchestrated by a plethora of molecules that detect the danger, signal intracellularly, and activate immune mechanisms to fight the threat. Understanding these processes at a level that allows to modulate their fate in a pathological context strongly relies on in vivo studies, as these can capture the complexity of the whole process and integrate the intricate interplay between the cellular and molecular actors of inflammation. Over the years, zebrafish has proven to be a well-recognized model to study immune responses linked to human physiopathology. We here provide a systematic review of the molecular effectors of inflammation known in this vertebrate and recapitulate their modes of action, as inferred from sterile or infection-based inflammatory models. We present a comprehensive analysis of their sequence, expression, and tissue distribution and summarize the tools that have been developed to study their function. We further highlight how these tools helped gain insights into the mechanisms of immune cell activation, induction, or resolution of inflammation, by uncovering downstream receptors and signaling pathways. These progresses pave the way for more refined models of inflammation, mimicking human diseases and enabling drug development using zebrafish models.

Identification and functional analysis of histone 1.2-like in red sea bream (Pagrus major)

Histone H1 acts as an essential chromatin component and participates in the formation of higher chromatin structures together with core histones. In addition, H1 also has important functions in physiological processes such as gene expression regulation, DNA repair, and the immune response. In this study, the histone homologous protein Pm-H1.2-like was identified from the transcriptome database of Pagrus major we studied previously. Conservatism of evolution was investigated by sequence alignment and phylogenetic analysis. Transcripts of Pm-H1.2-like were detected in P. major tissues. The highest expression level was found in gill and skin tissues. Consistent with the data from the transcriptome database, we observed that the expression of Pm-H1.2-like was rapidly induced in nonspecific cytotoxic cells (NCCs) infected with inactivated Vibrio anguillarum. Gene silencing of Pm-H1.2-like by RNAi significantly suppressed the expression of NK-lysin and GZMB in NCCs at 12 h after pathogen stimulation, but had no significant effect on IFN-γ expression. Next, we obtained the fusion proteins rPm-H1.2-like and rPm-H1.2-like (36-80) through prokaryotic expression. ELISA showed that rPm-H1.2-like bound to oligonucleotide (ODN) in a concentration-dependent manner, while no binding activity of rPm-H1.2-like (36-80) with ODN was observed. This study confirmed that Pm-H1.2-like actively participates in the immune response of NCCs to bacterial infection, deepening the understanding of the immune features of histone H1 in fish.

Nonspecific cytotoxic cell antimicrobial protein (NCAMP-1): a novel alarmin ligand identified in zebrafish

Cells from the coelomic cavity of adult zebrafish (zf) were used to study the alarmin-like activities of nonspecific cytotoxic cell antimicrobial protein-1 (NCAMP-1). Immunohistochemistry studies using polyclonal anti-NCAMP-1 identified constitutive NCAMP-1 in epithelial cells of the zf anterior kidney, in liver parenchyma and in the lamina propria of the intestine. NCAMP-1 was also located in the cytosol of mononuclear cells in these tissues. Cytosolic NCAMP-1 was detected in a diverse population of coelomic cells (CC) using confocal microscopy and polyclonal anti-NCAMP-1 staining. Large mononuclear and heterophil-like CC had intracellular NCAMP-1. These studies indicated that NCAMP-1 is constitutively found in epithelial cells and in ZFCC. To establish a relationship between NCAMP-1 and the alarmin functions of ATP, a stimulation-secretion model was initiated using zf coelomic cells (ZFCC). ZFCCs treated with the alarmin ATP secreted NCAMP-1 into culture supernatants. Treatment of ZFCC with either ATP or NCAMP-1 activated purinergic receptor induced pore formation detected by the ZFCC uptake of the dye YO-PRO-1. ATP induced YO-PRO-1 uptake was inhibited by antagonists oxidized-ATP, KN62, or CBB. These antagonists did not compete with NCAMP-1 induced YO-PRO-1 uptake. Binding of ZFCC by both ATP and NCAMP-1 produced an influx of Ca²⁺. Combined treatment of ZFCC with ATP and NCAMP-1 increased target cell cytotoxicity. Individually NCAMP-1 or ATP treatment did not produce target cell damage. Similar to ATP, NCAMP-1 activates cellular pore formation, calcium influx and cytotoxicity.

The teleost acute-phase inflammatory response and caspase activation by a novel alarmin-like ligand

This study tested the hypothesis that NCAMP-1 has alarmin-like properties and activates the caspase-1-binding site in cells of the teleost bone marrow (equivalent). In mammals, alarmins have been studied extensively; however, in teleosts, little is known about their identity and functions. Similar to alarmins, NCAMP-1 has a broad spectrum of bacteriolytic activity. NCAMP-1 is constitutively present in CF serum, and levels were increased following infection with Edwardsiella ictaluri Binding to AK cells was determined with rNCAMP-1 and an anti-His-tag antibody. In vitro treatment of AK (bone marrow equivalent) or spleen cells with rNCAMP-1 increased the IL-1β message three- to fivefold at 3 h, 6 h, and 9 h post-treatment. The association of NCAMP-1 with the activities of alarmin ATP and the acute inflammatory response was demonstrated by NCAMP-1-induced P2X₇R pore opening and YO-PRO-1 cellular influx. The association of NCAMP-1 binding with inflammasome activation was demonstrated by NCAMP-1 activation of the caspase-1-binding site for tetrapeptide Z-YVAD-FMK. In competition assays, this tetrapeptide competitively inhibited subsequent binding by the pan-caspase substrate tripeptide FAM-VAD-FMK. Lymphocyte-like cells from the spleen were 16%⁺, and epithelial cells were also positive for NCAMP-1. IHC staining and confocal microscopy confirmed the cytosolic existence of NCAMP-1 in lymphoreticular tissue and IL-1β in AK cells. CF T cell lines G14D and 28S.3 expressed NCAMP-1 in the cytosol and in storage granules. These studies strongly suggested that NCAMP-1 is an alarmin-like ligand with similar but distinct activities to those of ATP and HMGB-1.

Cell-free and cell-bound circulating nucleic acid complexes: mechanisms of generation, concentration and content

INTRODUCTION

Extracellular nucleic acids are found in human blood and cell culture medium as cell-free or being adsorbed at cell surface. In the last years, the circulating extracellular nucleic acids in blood were shown to be associated with certain diseases. Attempts are made to develop non-invasive methods of early tumor diagnostics based on analysis of circulating DNA and RNA.

AREAS COVERED

This article reviews accumulating data regarding cell-free and cell-surface-bound extracellular nucleic acid nature and generation mechanisms. Their existence as a constituent of the naturally occurring complexes with proteins or membrane-bearing particles is discussed with regard to their homeostatic concentration and distribution in healthy donor blood which are significantly altered in cancer patients. Gene-target and whole-genome studies reveal significant differences in gene representation between extracellular DNA and genome DNA. Overrepresentation of regions with high transcription activity has led to proposal that extracellular DNA generation is strongly dependent on the parent genome functionality, which is associated with chromosome packaging and DNA methylation levels.

EXPERT OPINION

Recent studies provide evidence of the circulating nucleome organization complexity indicating that discovery of extracellular DNA generation and circulation patterns in healthy condition and cancer is essential to enable the development of proper approaches for the selection of valid diagnostic markers.

Biomarker discovery and proteomic evaluation of cadmium toxicity on a collembolan species, Paronychiurus kimi (Lee)

The goal of this study was to identify promising new biomarkers of cadmium by identifying differentially expressed proteins in Paronychiurus kimi after exposure to cadmium. Through proteomic analysis of P. kimi using 1-D PAGE and nano-LC-MS/MS, 36 downregulated proteins and 40 upregulated proteins were found. Some of the downregulated and upregulated proteins were verified by LC-MS/MS analysis after 2-D PAGE. Downregulated proteins in response to cadmium exposure were involved in glycolysis and energy metabolism, chaperones, transcription, reproduction, and neuron growth. In contrast, proteins involved in glycolysis and energy production, neurogenesis, defense systems response to bacteria, and protein biosynthesis were upregulated in cadmium-treated collembolans. Cubulin may be a potential biomarker for the detection of cadmium in P. kimi since this biomarker was able to low levels (3.5 mg/kg) of cadmium. The 14-3-3 ζ was also found to be a potential biomarker for the detection of medium levels (14 mg/kg) of cadmium. Collembolans may be an alternative tool to humans because many collembolans proteins show a high homology to human proteins.

Origin, translocation and destination of extracellular occurring DNA--a new paradigm in genetic behaviour

The diagnostic value of extracellular occurring DNA (eoDNA) is limited by our lack of understanding its biological function. eoDNA exists in a number of forms, namely vesicle bound DNA (apoptotic bodies, micro particles, micro vesicles and exosomes), histone/DNA complexes or nucleosomes and virtosomes. These forms of DNA can also be categorized under the terms circulating DNA, cell free DNA, free DNA and extracellular DNA. The DNA can be released by means of form-specific mechanisms and seem to be governed by cell cycle phases and apoptosis. Active release is supported by evidence of energy dependent release mechanisms and various immunological- and messenger functions. Sequencing has shown that eoDNA sequences present in the nucleosome reflects traits and distribution of genome sequences and are regulated by ways of release and/or clearance. eoDNA enables the horizontal transfer of gene sequences from one cell to another, over various distances. The ability of eoDNA to partake in horizontal gene transfer makes it an important facet in the field of epigenetic variation. Clinical implementation of eoDNA diagnostics requires that all of the subgroups of eoDNA be properly investigated.