Boudinot Pierre

• PhD, Ing Agro INAPG
• Fish infection and immunity at French National Institute for Agriculture, Food, and Environment (INRAE)

Background This study focuses on genetic resistance to infectious pancreatic necrosis (IPN), a highly contagious disease caused by an aquatic birnavirus (IPNV) which especially affects salmonids worldwide. The objectives were to estimate the heritability of IPN resistance and to fine map quantitative trait loci (QTL) using a Bayesian Sparse Linear...

Members of the CD28 family are critical for the control of immune cell activation. While CD28 and CTLA4 were previously identified in teleost fish, most members of the CD28 family have been described only in tetrapods. Using a comparative genomics approach, we found (co)orthologs of all members of the CD28 family both in Chondrichthyes and basal Os...

In teleosts, the immunoglobulin classes produced by B cells are IgM, IgD, and IgT/IgZ. IgT was initially described as an immunoglobulin specialized in mucosal responses; accumulating evidence, however, shows that it is also involved in systemic immune responses. Two types of IgT/IgZ (IgT1 and IgT2) were previously described in common carp, but thei...

Cells are equipped with intracellular RIG-like Receptors (RLRs) detecting double stranded (ds)RNA, a molecule with Pathogen-Associated Molecular Pattern (PAMPs) generated during the life cycle of many viruses. Melanoma Differentiation-Associated protein 5 (MDA5), a helicase enzyme member of the RLRs encoded by the ifih1 gene, binds to long dsRNA mo...

Contexte Les maladies virales représentent une menace pour l’essor de la pisciculture. Leur contrôle dépend fortement de la disponibilité en lignées cellulaires capables de produire des particules virales pour le diagnostic, l‘infectiologie et la production vaccinale. A l’heure actuelle, de nombreux virus affectant les piscicultures n’ont pas de li...

dsRNA-dependent protein kinase R (PKR) is a key factor of innate immunity. It is involved in translation inhibition, apoptosis, and enhancement of the proinflammatory and IFN responses. However, how these antiviral functions are conserved during evolution remains largely unknown. Overexpression and knockout studies in a Chinook salmon (Oncorhynchus...

Background Viperin, also known as radical S-adenosyl-methionine domain containing protein 2 (RSAD2), is an interferon-inducible protein that is involved in the innate immune response against a wide array of viruses. In mammals, Viperin exerts its antiviral function through enzymatic conversion of cytidine triphosphate (CTP) into its antiviral analo...

Uncovering the epigenomic regulation of immune responses is essential for a comprehensive understanding of host defence mechanisms, though remains poorly investigated in farmed fish. We report the first annotation of the innate immune regulatory response in the turbot genome (Scophthalmus maximus), integrating RNA-Seq with ATAC-Seq and ChIP-Seq (H3...

The CD28-B7 interaction is required to deliver a second signal necessary for T-cell activation. Additional membrane receptors of the CD28 and B7 families are also involved in immune checkpoints that positively or negatively regulate leukocyte activation, in particular T lymphocytes. BTLA is an inhibitory receptor that belongs to a third receptor fa...

Germinal centers (GCs) or analogous secondary lymphoid microstructures (SLMs) are thought to have evolved in endothermic species. However, living representatives of their ectothermic ancestors can mount potent secondary antibody (Ab) responses upon infection or immunization, despite the apparent lack of SLMs in these cold-blooded vertebrates. How a...

The interferon-induced antiviral response is mediated through a wide range of Interferon-Stimulated Genes (ISGs). The double-stranded RNA-activated Protein Kinase R (PKR), one of the most studied proteins encoded by an ISG, is recognized as a multifunctional key factor of innate immunity. In mammals, it is involved in central cellular processes in...

Cells are equipped with intracellular RIG-like Receptors (RLRs) detecting double stranded (ds)RNA, a molecule with Pathogen-Associated Molecular Pattern (PAMPs) present in the cell during the life cycle of many viruses. Melanoma Differentiation-Associated protein 5 (MDA5), a helicase enzyme member of the RLRs encoded by the ifih1 gene, binds to lon...

Cells are equipped with intracellular RIG-like Receptors (RLRs) detecting double stranded (ds)RNA, a molecule with Pathogen-Associated Molecular Pattern (PAMPs) present in the cell during the life cycle of many viruses. Melanoma Differentiation-Associated protein 5 (MDA5), a helicase enzyme member of the RLRs encoded by the ifih1 gene, binds to lon...

Toll-like receptors (TLRs) are a class of pattern recognition receptors (PRRs) that can recognize pathogen- and damage-associated molecular patterns (PAMPs and DAMPs). They selectively recruit distinct adapter molecules including myeloid differentiation primary response protein 88 (MyD88) and TIR domain-containing adaptor-inducing interferon-beta (...

The antiviral response is mediated through the expression of a wide range of interferon-stimulated genes (ISGs). The radical S-adenosyl-methionine domain-containing protein 2 (Rsad2), also known as Viperin, is a wellknown ISG-encoded protein with a potent antiviral activity across species and cell types. In mammals, Viperin exerts its function thro...

T-cell mediated immunity relies on a vast array of antigen specific T cell receptors (TR). Characterizing the structure of TR loci is essential to study the diversity and composition of T cell responses in vertebrate species. The lack of good-quality genome assemblies, and the difficulty to perform a reliably mapping of multiple highly similar TR s...

Focal dark spots (DS) in farmed Atlantic salmon fillets contain a significant number of B cells as revealed by the high abundance of immunoglobulin (Ig) transcripts in transcriptome data. The immune response in DS remains unknown while they represent a major problem in commercial aquaculture. Here, we characterized the diversity and clonal composit...

CD9 is a member of the tetraspanin family, which is characterised by a unique domain structure and conserved motifs. In mammals, CD9 is found in tetraspanin-enriched microdomains (TEMs) on the surface of virtually every cell type. CD9 has a wide variety of roles, including functions within the immune system. Here we show the first in-depth analysis...

The constant exposure of the fish branchial cavity to aquatic pathogens must have driven local mucosal immune responses to be extremely important for their survival. In this study, we used a universal marker for T lymphocytes/natural killer cells (ZAP70) and advanced imaging techniques to investigate the lymphoid architecture of the zebrafish branc...

Infectious diseases are a major constraint on aquaculture. Genetic lines with different susceptibilities to diseases are useful models to identify resistance mechanisms to pathogens and to improve prophylaxis. Bacterial cold-water disease (BCWD) caused by Flavobacterium psychrophilum represents a major threat for freshwater salmonid farming worldwi...

The signals controlling marginal zone (MZ) and follicular (FO) B cell development remain incompletely understood. Here, we show that AKT orchestrates MZ B cell formation in mice and humans. Genetic models that increase AKT signaling in B cells or abolish its impact on FoxO transcription factors highlight the AKT-FoxO axis as an on-off switch for MZ...

Infectious diseases are a major constraint on aquaculture. Genetic lines with different susceptibilities to diseases are useful models to identify resistance mechanisms to pathogens and to improve prophylaxis. Bacterial cold-water disease (BCWD) caused by Flavobacterium psychrophilum represents a major threat for freshwater salmonid farming worldwi...

Toll‐like receptors (TLR) control the activation of dendritic cells that prime CD4⁺ T cells in draining lymph nodes, where these T cells then undergo massive clonal expansion. The mechanisms controlling this clonal T cell expansion are poorly defined. Using the CD4⁺ T cell‐mediated disease experimental autoimmune encephalomyelitis (EAE), we show he...

The liver is a multitasking organ with essential functions for vertebrate health spanning metabolism and immunity. In contrast to mammals, our understanding of liver cellular heterogeneity and its role in regulating immunological status remains poorly defined in fishes. Addressing this knowledge gap, we generated a transcriptomic atlas of 47,432 nu...

We studied cell recruitment following optic tectum (OT) injury in zebrafish (Danio rerio), which has a remarkable ability to regenerate many of its organs, including the brain. The OT is the largest dorsal layered structure in the zebrafish brain. In juveniles, it is an ideal structure for imaging and dissection. We investigated the recruited cells...

CD4⁺FOXP3⁺ Tregs are currently explored to develop cell therapies against immune‐mediated disorders, with an increasing focus on antigen receptor‐engineered Tregs. Deciphering their mode of action is necessary to identify the strengths and limits of this approach. Here, we addressed this issue in an autoimmune disease of the CNS, EAE. Following dis...

Upon infection, B lymphocytes develop clonal responses. In teleost fish, which lack lymph nodes, the kinetics and location of B cell responses remain poorly characterized. Fish pronephros is the site of B cell differentiation and the main niche for persistence of plasma cells. In this study, we undertook the analysis of the rainbow trout IgHμ reper...

This chapter reviews the particular features of teleost fish immunoglobulins, their B cells, and B-cell repertoires. We first review the current knowledge regarding teleost Ig genes, Ig proteins, and B-cell populations in the context of the diversity of this taxonomic group, the largest among vertebrates. We then describe how the development of seq...

The term “major histocompatibility complex” (MHC) was used originally to name a polymorphic genetic region in mammals, several loci of which were involved in determining acute allograft rejection, hence the term histocompatibility. “MHC molecules” commonly refers to a special class of proteins expressed at the surface of somatic cells and involved...

Animal models are essential to understanding COVID-19 pathophysiology and for preclinical assessment of drugs and other therapeutic or prophylactic interventions. We explored the small, cheap, and transparent zebrafish larva as a potential host for SARS-CoV-2. Bath exposure, as well as microinjection in the coelom, pericardium, brain ventricle, or...

In this work, we describe the complete repertoire of channel catfish, Ictalurus punctatus, IFNs and IFN receptor genes. Based on multiple genomic and transcriptomic resources we identified 16 type I IFN genes, which represent the six type I IFN subgroups previously defined in salmonids (a-f.) No representatives of subgroup h previously only found i...

Anosmia, loss of smell, is a prevalent symptom of SARS-CoV-2 infection. Anosmia may be explained by several mechanisms driven by infection of non-neuronal cells and damage in the nasal epithelium rather than direct infection of olfactory sensory neurons (OSNs). Previously, viral proteins have been shown to be sufficient to cause neuroimmune respons...

B30.2 domains, also known as PRY/SPRY, are key components of specific subsets of two large families of proteins involved in innate immunity: the tripartite motif proteins (TRIMs) and the Nod-like receptors (NLRs). TRIM proteins are important, often inducible factors of antiviral innate immunity, targeting multiple steps of viral cycles through a va...

The zebrafish is extensively used as an animal model for human and fish diseases. However, our understanding of the structural organization of its immune system remains incomplete, especially the mucosa-associated lymphoid tissues (MALTs). Teleost MALTs are commonly perceived as diffuse and scattered populations of immune cells throughout the mucos...

In jawed vertebrates, two major T cell populations have been characterized. They are defined as α/β or γ/δ T cells, based on the expressed T cell receptor. Salmonids (family Salmonidae) include two key teleost species for aquaculture, rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) which constitute important models for fish im...

The repertoire of Abs is generated by genomic rearrangements during B cell differentiation. Although V(D)J rearrangements lead to repertoires mostly different between individuals, recent studies have shown that they contain a substantial fraction of overrepresented and shared "public" clones. We previously reported a strong public IgHμ clonotypic r...

Animal models are essential to understand COVID-19 pathophysiology and for pre-clinical assessment of drugs and other therapeutic or prophylactic interventions. We explored the small, cheap and transparent zebrafish larva as a potential host for the SARS-CoV-2 virus. Bath exposure, as well as microinjection in the coelom, pericardium, brain ventric...

Tilapia lake virus (TiLV; genus: Tilapinevirus, family: Amnoonviridae) is a recently characterised enveloped virus with a linear, negative-sense single-stranded RNA genome, which causes high mortality in tilapia species. In the present study, we demonstrated that zebrafish (Danio rerio) larvae are susceptible to TiLV infection upon sys-temic inject...

The stat gene family diversified during early vertebrate evolution thanks to two rounds of whole genome duplication (WGD) to produce a typical repertoire composed of 6 STAT factors (named 1–6). In contrast, only one or two stat genes have been reported in C. elegans and in D. melanogaster. The main types of STAT found from bony fish to mammals are...

Interferon regulatory factors (IRFs) as a family, are major regulators of the innate antiviral response in vertebrates principally involved in regulating the expression of interferons (IFNs) and interferon-stimulated genes (ISGs). To date, nine IRFs have been identified in mammals with a 10th member also found in several avian and fish species. Thr...

Background In zebrafish, lymphatic endothelial cells (LECs) originate from multiple/several distinct progenitor populations and generate organ‐specific lymphatic vasculatures. Cell fate and tissue specificities were determined using a combination of genetically engineered transgenic lines in which the promoter of a LEC‐specific gene drives expressi...

High-throughput sequencing technologies brought a renewed interest for immune repertoires. Fish Ab and B cell repertoires are no exception, and their comprehensive analysis can both provide new insights into poorly understood immune mechanisms, and identify markers of protection after vaccination. However, the lack of genomic description and standa...

18 19 The COVID-19 pandemic has prompted the search for animal models that recapitulate the 20 pathophysiology observed in humans infected with SARS-CoV-2 and allow rapid and high 21 throughput testing of drugs and vaccines. Exposure of larvae to SARS-CoV-2 Spike (S) receptor 22 binding domain (RBD) recombinant protein was sufficient to elevate lar...

18 19 The COVID-19 pandemic has prompted the search for animal models that recapitulate the 20 pathophysiology observed in humans infected with SARS-CoV-2 and allow rapid and high 21 throughput testing of drugs and vaccines. Exposure of larvae to SARS-CoV-2 Spike (S) receptor 22 binding domain (RBD) recombinant protein was sufficient to elevate lar...

Infectious diseases represent a major threat for the sustainable development of fish farming. Efficient vaccines are not available against all diseases, and growing antibiotics resistance limits the use of antimicrobial drugs in aquaculture. It is therefore important to understand the basis of fish natural resistance to infections to help genetic s...

Background: Genome editing is transforming bioscience research, but its application to non-model organisms, such as farmed animal species, requires optimisation. Salmonids are the most important aquaculture species by value, and improving genetic resistance to infectious disease is a major goal. However, use of genome editing to evaluate putative...

In bony fish, the gill filaments are essential for gas exchanges, but also are vulnerable to infection by water-borne microorganisms. Omnipresent across fish, gill-associated lymphoid tissues (GIALT) regulate interactions with local microbiota and halt infection by pathogens. A special GIALT structure has recently been found in Salmonids, the inter...

Inflammation is an essential part of immunity against pathogens and tumors but can promote disease if not tightly regulated. Self and non-self-nucleic acids can trigger inflammation, through recognition by the cyclic GMP-AMP (cGAMP) synthetase (cGAS) and subsequent activation of the stimulator of interferon genes (STING) protein. Here, we show that...

Induction of adaptive immune responses in higher vertebrate species occur within organized lymphoid structures (e.g. lymph nodes, Peyer’s patches). It has been proposed that such structures emerged throughout evolutionary time with the goal to maximize encounters between antigens, antigens-presenting cells and B-T lymphocytes. Fish lack such struct...

Vaccine adjuvants induce host innate immune responses improving long-lasting adaptive immunity against vaccine antigens. In vitro models can be used to compare these responses between adjuvants and the infection targeted by the vaccine. We utilized transcriptomic profiling of an Atlantic salmon cell line to compare innate immune responses against I...

P2X purinergic receptors are extracellular ATP-gated ion channel receptors present on the cell plasma membrane. P2X receptors have been found in Metazoa, fungi, amoebas, and in plants. In mammals, P2X7 is expressed by a large number of cell types and is involved in inflammation and immunity. Remarkably, P2X7 does not desensitize as other P2X do, a...

After publication of this work [1], we noted that there was an error in Table 3 Line 4.

Long-term immunity is of great importance for protection against pathogens and has been extensively studied in mammals. Successive heterologous infections can affect the maintenance of immune memory, inducing attrition of T memory cells and diminishing B cell mediated protection. In fish, the basis of immune memory and the mechanisms of immunizatio...

The evolution of the IFN system, the major innate antiviral mechanism of vertebrates, remains poorly understood. According to the detection of type I IFN genes in cartilaginous fish genomes, the system appeared 500 My ago. However, the IFN system integrates many other components, most of which are encoded by IFN-stimulated genes (ISGs). To shed lig...

In teleost fish as in mammals, humoral adaptive immunity is based on B lymphocytes expressing highly diverse immunoglobulins (IG). During B cell differentiation, IG loci are subjected to genomic rearrangements of V, D, and J genes, producing a unique antigen receptor expressed on the surface of each lymphocyte. During the course of an immune respon...

Extracellular nucleotides are important mediators of cell activation and trigger multiple responses via membrane receptors known as purinergic receptors (P2). P2X receptors are ligand-gated ion channels, activated by extracellular ATP. P2X4 is one of the most sensitive purinergic receptors, that is typically expressed by neurons, microglia, and som...

Genome editing is transforming bioscience research, but its application to non-model organisms, such as farmed animal species, requires optimisation. Salmonids are the most important aquaculture species by value, and improving genetic resistance to infectious disease is a major goal. However, use of genome editing to evaluate putative disease resis...

Bony fish represent the most basal vertebrate branch with a dedicated mucosal immune system, which comprises immunologically heterogeneous microenvironments armed with innate and adaptive components. In rainbow trout (Oncorhynchus mykiss), a nasopharynx-associated lymphoid tissue (NALT) was recently described as a diffuse network of myeloid and lym...

The rabbit has been widely used in immunology and infectiology. Rabbit immunoglobulins have been extensively studied, leading to the discovery of their idiotypes, allotypic diversity, and of the diversification of the primary repertoire by hyperconversion. Much less is known about rabbit T cell receptors (TR), especially TRA. This isotype is partic...

The evolution of the interferon (IFN) system, the major innate antiviral mechanism of vertebrates, remains poorly understood. According to the detection of type I IFN genes in cartilaginous fish genomes, the system appeared 500My ago. However, the IFN system integrates many other components, most of which are encoded by IFN-stimulated genes (ISGs)....

IFN belong to a group of cytokines specialized in the immunity to viruses. Upon viral infection, type I IFN is produced and alters the transcriptome of responding cells through induction of a set of IFN stimulated genes (ISGs) with regulatory or antiviral function, resulting in a cellular antiviral state. Fish genomes have both type I IFN and type...

Our previous work has shown the existence of distinct subsets of B cells in vertebrates that are highly phagocytic. To understand further the involvement of B cells in other potential innate immune functions, we performed the first comparative transcriptome analysis on FACS-sorted IgT+ and IgM+ B cells in rainbow trout, a primitive teleost fish spe...

The overarching structure of the type I interferon (IFN) system is conserved across vertebrates. However, the variable numbers of whole genome duplication events during fish evolution offer opportunities for the expansion, diversification, and new functionalization of the genes that are involved in antiviral immunity. In this review, we examine how...

The production of piscine viruses, in particular of koi herpesvirus (KHV, CyHV‐3) and infectious salmon anaemia virus (ISAV), is still challenging due to the limited susceptibility of available cell lines to these viruses. A number of cell lines from different fish species were compared to standard diagnostic cell lines for KHV and ISAV regarding t...

Background Bacterial cold-water disease, which is caused by Flavobacterium psychrophilum, is one of the major diseases that affect rainbow trout (Oncorhynchus mykiss) and a primary concern for trout farming. Better knowledge of the genetic basis of resistance to F. psychrophilum would help to implement this trait in selection schemes and to investi...

Tripartite motif (TRIM) family or RBCC proteins comprises characteristic zinc‐binding domains (a RING (R), a B‐box type 1 (B1) and a B‐box type 2 (B2)) and coiled‐coil (CC) domain followed by a C-terminus variable domain. There are about 80 different TRIM proteins in human, but more than 200 in zebrafish with several large gene expansions (ftr >70...

Innate lymphoid cells (ILCs) are important mediators of the immune response and homeostasis in barrier tissues of mammals. However, the existence and function of ILCs in other vertebrates are poorly understood. Here, we use single-cell RNA sequencing to generate a comprehensive atlas of zebrafish lymphocytes during tissue homeostasis and after immu...

Vaccination induces “public” antibody clonotypes common to all individuals of a species, that may mediate universal protection against pathogens. Only few studies tried to trace back the origin of these public B-cell clones. Here we used Illumina sequencing and computational modeling to unveil the mechanisms shaping the structure of the fish memory...