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Article ; Online: Phylogeny and expression of tetraspanin CD9 paralogues in rainbow trout (Oncorhynchus mykiss).

Dehler, Carola E / Boudinot, Pierre / Collet, Bertrand / Martin, SamuelA M

Developmental and comparative immunology

2023 Volume 146, Page(s) 104735

Abstract: 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 ... ...

Abstract	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 of the cd9 gene family in salmonids, showing that this gene has expanded to six paralogues in three groups (cd9a, cd9b, cd9c) through whole genome duplication events. We suggest that through genome duplications, cd9 has undergone subfunctionalisation in the paralogues and that cd9c1 and cd9c2 in particular are involved in antiviral responses in salmonid fish. We show that these paralogues are significantly upregulated in parallel to classic interferon-stimulated genes (ISGs) active in the antiviral response. Expression analysis of cd9 may therefore become an interesting target to assess teleost responses to viruses.
MeSH term(s)	Animals ; Oncorhynchus mykiss ; Phylogeny ; Genome ; Tetraspanins/genetics ; Tetraspanins/metabolism ; Antiviral Agents/metabolism ; Mammals/genetics
Chemical Substances	Tetraspanins ; Antiviral Agents
Language	English
Publishing date	2023-05-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	752411-0
ISSN	1879-0089 ; 0145-305X
ISSN (online)	1879-0089
ISSN	0145-305X
DOI	10.1016/j.dci.2023.104735
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Article ; Online: Phylogeny and expression of tetraspanin CD9 paralogues in rainbow trout (Oncorhynchus mykiss)

Dehler, Carola E. / Boudinot, Pierre / Collet, Bertrand / Martin, SamuelA.M.

Developmental and Comparative Immunology. 2023 Sept., v. 146 p.104735-

2023

Abstract	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 of the cd9 gene family in salmonids, showing that this gene has expanded to six paralogues in three groups (cd9a, cd9b, cd9c) through whole genome duplication events. We suggest that through genome duplications, cd9 has undergone subfunctionalisation in the paralogues and that cd9c1 and cd9c2 in particular are involved in antiviral responses in salmonid fish. We show that these paralogues are significantly upregulated in parallel to classic interferon-stimulated genes (ISGs) active in the antiviral response. Expression analysis of cd9 may therefore become an interesting target to assess teleost responses to viruses.
Keywords	Oncorhynchus mykiss ; genes ; immune system ; immunology ; phylogeny ; Salmonids ; CD9 ; Whole genome duplication
Language	English
Dates of publication	2023-09
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Use and reproduction
ZDB-ID	752411-0
ISSN	1879-0089 ; 0145-305X
ISSN (online)	1879-0089
ISSN	0145-305X
DOI	10.1016/j.dci.2023.104735
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Article ; Online: Gut Associated Lymphoid Tissue (GALT) primary cells and stable cell lines as predictive models for intestinal health in rainbow trout (<i>Oncorhynchus mykiss</i>).

Porter, D / Peggs, David / McGurk, C / Martin, Samuel A M

Frontiers in immunology

2022 Volume 13, Page(s) 1023235

Abstract: The use of functional feeds for farmed fish is now regarded as a key factor in improving fish health and performance against infectious disease. However, the mechanisms by which these nutritional components modulate the immune response are not fully ... ...

Abstract	The use of functional feeds for farmed fish is now regarded as a key factor in improving fish health and performance against infectious disease. However, the mechanisms by which these nutritional components modulate the immune response are not fully understood. The present study was undertaken to identify the suitability of both primary gut-associated lymphoid tissue (GALT) leucocyte cells and established rainbow trout cell lines as potential alternative methods to test functional feed ingredients prior to full fish feeding trials that can take months to complete. In addition to the primary GALT culture cells, the two rainbow cell lines RTS11 and RTgutGC which are from macrophage and gut epithelial cells, respectively. The cells were stimulated with a variety of pathogen associated molecular patterns (PAMPs) (PHA and Poly I:C) and recombinant rainbow trout IL-1β (rIL-1β), a proinflammatory cytokine, additionally two forms of β-glucan, a prebiotic commonly used aquafeeds were used as stimulants. From this, the suitability of cell models as a health screen for functional feeds was assessed. GALT leucocytes were deemed most effective to act as a health screen over the 4hr time point demonstrating responses to Poly I:C, PHA, and rIL-1β. RTS11 and RTgutGC also responded to the stimulants but did not give a strong T-cell response, most likely reflecting the nature of the cell type as opposed to the mixed cell populations from the primary GALT cell cultures. When stimulated with both forms of β-glucan, GALT leucocytes demonstrated a strong proinflammatory and T-cell response.
MeSH term(s)	Animals ; Oncorhynchus mykiss ; Cell Line ; Poly I-C/metabolism ; beta-Glucans/metabolism ; Lymphoid Tissue
Chemical Substances	Poly I-C (O84C90HH2L) ; beta-Glucans
Language	English
Publishing date	2022-10-20
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2022.1023235
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Article: Interactive effects of dietary lipid and nutritional emulsifier supplementation on growth, chemical composition, immune response and lipid metabolism of juvenile Nile tilapia (Oreochromis niloticus)

Wangkahart, Eakapol / Bruneel, Brecht / Wisetsri, Tanakrit / Nontasan, Supap / Martin, Samuel A.M. / Chantiratikul, Anut

Elsevier B.V. Aquaculture. 2022 Jan. 15, v. 546

2022

Abstract: The objective of this study was to investigate the interactive effects of supplementation with different levels of dietary lipids and a commercial nutritional emulsifier (NE) on the growth, feed utilization, immune response and lipid metabolism of ... ...

Abstract	The objective of this study was to investigate the interactive effects of supplementation with different levels of dietary lipids and a commercial nutritional emulsifier (NE) on the growth, feed utilization, immune response and lipid metabolism of juvenile Nile tilapia (Oreochromis niloticus). A 5 × 2 factorial design was formulated with five lipid supplement levels (0, 15, 30, 45 and 60 g/kg) and NE supplementation (with or without NE at 0.35 g/kg). Nile tilapia with an initial average body weight of 8.06 g were randomly placed in 30 cages and offered one of the ten diets for 8 weeks. The results show that dietary NE supplementation significantly increased the final weight, weight gain and specific growth rate compared with fish fed diets without NE (P<0.05). Interestingly, dietary NE supplementation significantly improved the feed conversion ratio (P<0.05). The supplementation of diets with NE significantly reduced the cholesterol levels (P<0.05). The activities of catalase, superoxide dismutase and glutathione peroxidase significantly decreased as dietary lipid supplement levels increased, but they were significantly improved by dietary NE supplementation (P<0.05). The results also show that the liver malondialdehyde (MDA) content significantly increased as lipid supplement levels increased, while NE supplementation resulted in significantly decreased MDA levels (P<0.05). As dietary lipid supplement levels increased, the crude lipid content of the fillet significantly increased in fish fed a diet supplemented with NE (P<0.05). Moreover, lipase activity was significantly increased when the diet was supplemented with NE (P<0.05). A total of 20 fatty acids were measured in the fillets of fish fed diets supplemented with different lipid levels and NE. Significantly higher levels of polyunsaturated fatty acids, particularly linoleic acid (18:2 n6c), γ-linolenic acid (C18:3 n6) and α-linolenic acid (C18:3 n3), were found in fish fed diets supplemented with NE. In summary, dietary NE supplementation has a positive effect on feed digestion and absorption, resulting in improved fish growth performance, immune response and nutritional value of the muscle due to increased essential fatty acid contents. NE supplementation is particularly effective when it is added to diets with low lipid levels.
Keywords	Oreochromis niloticus ; absorption ; animal growth ; aquaculture ; body weight ; carboxylic ester hydrolases ; catalase ; cholesterol ; dietary fat ; digestion ; emulsifiers ; feed conversion ; fillets ; fish ; glutathione peroxidase ; growth performance ; immune response ; juveniles ; linoleic acid ; lipid content ; lipid metabolism ; liver ; malondialdehyde ; muscles ; nutritive value ; specific growth rate ; superoxide dismutase ; weight gain
Language	English
Dates of publication	2022-0115
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	185380-6
ISSN	0044-8486 ; 0044-8516
ISSN	0044-8486 ; 0044-8516
DOI	10.1016/j.aquaculture.2021.737341
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Article: Microbiomes in the context of developing sustainable intensified aquaculture.

Lorgen-Ritchie, Marlene / Uren Webster, Tamsyn / McMurtrie, Jamie / Bass, David / Tyler, Charles R / Rowley, Andrew / Martin, Samuel A M

Frontiers in microbiology

2023 Volume 14, Page(s) 1200997

Abstract: With an ever-growing human population, the need for sustainable production of nutritional food sources has never been greater. Aquaculture is a key industry engaged in active development to increase production in line with this need while remaining ... ...

Abstract	With an ever-growing human population, the need for sustainable production of nutritional food sources has never been greater. Aquaculture is a key industry engaged in active development to increase production in line with this need while remaining sustainable in terms of environmental impact and promoting good welfare and health in farmed species. Microbiomes fundamentally underpin animal health, being a key part of their digestive, metabolic and defense systems, in the latter case protecting against opportunistic pathogens in the environment. The potential to manipulate the microbiome to the advantage of enhancing health, welfare and production is an intriguing prospect that has gained considerable traction in recent years. In this review we first set out what is known about the role of the microbiome in aquaculture production systems across the phylogenetic spectrum of cultured animals, from invertebrates to finfish. With a view to reducing environmental footprint and tightening biological and physical control, investment in "closed" aquaculture systems is on the rise, but little is known about how the microbial systems of these closed systems affect the health of cultured organisms. Through comparisons of the microbiomes and their dynamics across phylogenetically distinct animals and different aquaculture systems, we focus on microbial communities in terms of their functionality in order to identify what features within these microbiomes need to be harnessed for optimizing healthy intensified production in support of a sustainable future for aquaculture.
Language	English
Publishing date	2023-06-23
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2023.1200997
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Article ; Online: Catch of the Day: New Serum Amyloid A (SAA) Antibody Is a Valuable Tool to Study Fish Health in Salmonids.

Buks, Ralfs / Alnabulsi, Abdo / Zindrili, Rodanthi / Alnabulsi, Ayham / Wang, Alex / Wang, Tiehui / Martin, Samuel A M

Cells

2023 Volume 12, Issue 16

Abstract: Serum amyloid A (SAA) proteins belong to a family of acute-phase reactants, playing an integral role in defending the organism from pathological damage. Despite a wealth of data on the regulation of SAA transcripts in teleosts, there is only limited ... ...

Abstract	Serum amyloid A (SAA) proteins belong to a family of acute-phase reactants, playing an integral role in defending the organism from pathological damage. Despite a wealth of data on the regulation of SAA transcripts in teleosts, there is only limited information on these proteins' abundance in fish. The aim of this study is to characterise SAA protein levels in salmonids using a newly developed antibody specific to salmonid SAA. The salmonid SAA antibody detected SAA and accurately discriminated between stimulated and control specimens from rainbow trout macrophage cell line (RTS-11) in vitro, as well as rainbow trout challenged with
MeSH term(s)	Animals ; Serum Amyloid A Protein ; Antibodies ; Oncorhynchus mykiss ; Acute-Phase Proteins ; Enzyme-Linked Immunosorbent Assay
Chemical Substances	Serum Amyloid A Protein ; Antibodies ; Acute-Phase Proteins
Language	English
Publishing date	2023-08-19
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells12162097
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Article ; Online: Fur removal promotes an earlier expression of involution-related genes in mammary gland of lactating mice.

Król, Elżbieta / Turner, Frances / Derous, Davina / Mitchell, Sharon E / Martin, Samuel A M / Douglas, Alex / Speakman, John R

Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology

2023 Volume 193, Issue 2, Page(s) 171–192

Abstract: Peak lactation occurs when milk production is at its highest. The factors limiting peak lactation performance have been subject of intense debate. Milk production at peak lactation appears limited by the capacity of lactating females to dissipate body ... ...

Abstract	Peak lactation occurs when milk production is at its highest. The factors limiting peak lactation performance have been subject of intense debate. Milk production at peak lactation appears limited by the capacity of lactating females to dissipate body heat generated as a by-product of processing food and producing milk. As a result, manipulations that enhance capacity to dissipate body heat (such as fur removal) increase peak milk production. We investigated the potential correlates of shaving-induced increases in peak milk production in laboratory mice. By transcriptomic profiling of the mammary gland, we searched for the mechanisms underlying experimentally increased milk production and its consequences for mother-young conflict over weaning, manifested by advanced or delayed involution of mammary gland. We demonstrated that shaving-induced increases in milk production were paradoxically linked to reduced expression of some milk synthesis-related genes. Moreover, the mammary glands of shaved mice had a gene expression profile indicative of earlier involution relative to unshaved mice. Once provided with enhanced capacity to dissipate body heat, shaved mice were likely to rear their young to independence faster than unshaved mothers.
MeSH term(s)	Female ; Animals ; Mice ; Lactation ; Mammary Glands, Animal/metabolism ; Milk/metabolism
Language	English
Publishing date	2023-01-18
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	231245-1
ISSN	1432-136X ; 0174-1578
ISSN (online)	1432-136X
ISSN	0174-1578
DOI	10.1007/s00360-023-01474-9
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Article ; Online: Nutrigenomics and immune function in fish: new insights from omics technologies.

Martin, Samuel A M / Król, Elżbieta

Developmental and comparative immunology

2017 Volume 75, Page(s) 86–98

Abstract: The interplay between nutrition and immune system is well recognised, however the true integration of research between nutrition, animal energy status and immune function is still far from clear. In fish nutrition, especially for species maintained in ... ...

Abstract	The interplay between nutrition and immune system is well recognised, however the true integration of research between nutrition, animal energy status and immune function is still far from clear. In fish nutrition, especially for species maintained in aquaculture, formulated feeds are significantly different from the natural diet with recent changes in nutrient sources, especially with protein and oil sources now being predominated by terrestrial derived ingredients. Additionally, many feeds are now incorporated to health management and termed functional feeds, which are believed to improve fish health, reduce disease outbreaks and/or improve post-infection recovery. Using new omics technologies, including transcriptomics (microarray and RNA-seq) and proteomics, the impacts of nutrition on the immune system is becoming clearer. By using molecular pathway enrichment analysis, modules of genes can indicate how both local (intestinal) and systemic immune function are being altered. Although great progress has been made to define the changes in host immune function, understanding the interplay between fish nutrition, intestinal microbiome and immune system is only just beginning to emerge.
MeSH term(s)	Animals ; Aquaculture ; Fishes/genetics ; Fishes/immunology ; Gastrointestinal Microbiome ; Gene Regulatory Networks/genetics ; Genomics ; High-Throughput Nucleotide Sequencing ; Immunity/genetics ; Microarray Analysis ; Nutritional Physiological Phenomena/genetics ; Signal Transduction ; Transcriptome
Language	English
Publishing date	2017-02-28
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	752411-0
ISSN	1879-0089 ; 0145-305X
ISSN (online)	1879-0089
ISSN	0145-305X
DOI	10.1016/j.dci.2017.02.024
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Article ; Online: Mapping the cellular landscape of Atlantic salmon head kidney by single cell and single nucleus transcriptomics.

Andresen, Adriana M S / Taylor, Richard S / Grimholt, Unni / Daniels, Rose Ruiz / Sun, Jianxuan / Dobie, Ross / Henderson, Neil C / Martin, Samuel A M / Macqueen, Daniel J / Fosse, Johanna H

Fish & shellfish immunology

2024 Volume 146, Page(s) 109357

Abstract: Single-cell transcriptomics is the current gold standard for global gene expression profiling, not only in mammals and model species, but also in non-model fish species. This is a rapidly expanding field, creating a deeper understanding of tissue ... ...

Abstract	Single-cell transcriptomics is the current gold standard for global gene expression profiling, not only in mammals and model species, but also in non-model fish species. This is a rapidly expanding field, creating a deeper understanding of tissue heterogeneity and the distinct functions of individual cells, making it possible to explore the complexities of immunology and gene expression on a highly resolved level. In this study, we compared two single cell transcriptomic approaches to investigate cellular heterogeneity within the head kidney of healthy farmed Atlantic salmon (Salmo salar). We compared 14,149 cell transcriptomes assayed by single cell RNA-seq (scRNA-seq) with 18,067 nuclei transcriptomes captured by single nucleus RNA-Seq (snRNA-seq). Both approaches detected eight major cell populations in common: granulocytes, heamatopoietic stem cells, erythrocytes, mononuclear phagocytes, thrombocytes, B cells, NK-like cells, and T cells. Four additional cell types, endothelial, epithelial, interrenal, and mesenchymal cells, were detected in the snRNA-seq dataset, but appeared to be lost during preparation of the single cell suspension submitted for scRNA-seq library generation. We identified additional heterogeneity and subpopulations within the B cells, T cells, and endothelial cells, and revealed developmental trajectories of heamatopoietic stem cells into differentiated granulocyte and mononuclear phagocyte populations. Gene expression profiles of B cell subtypes revealed distinct IgM and IgT-skewed resting B cell lineages and provided insights into the regulation of B cell lymphopoiesis. The analysis revealed eleven T cell sub-populations, displaying a level of T cell heterogeneity in salmon head kidney comparable to that observed in mammals, including distinct subsets of cd4/cd8-negative T cells, such as tcrγ positive, progenitor-like, and cytotoxic cells. Although snRNA-seq and scRNA-seq were both useful to resolve cell type-specific expression in the Atlantic salmon head kidney, the snRNA-seq pipeline was overall more robust in identifying several cell types and subpopulations. While scRNA-seq displayed higher levels of ribosomal and mitochondrial genes, snRNA-seq captured more transcription factor genes. However, only scRNA-seq-generated data was useful for cell trajectory inference within the myeloid lineage. In conclusion, this study systematically outlines the relative merits of scRNA-seq and snRNA-seq in Atlantic salmon, enhances understanding of teleost immune cell lineages, and provides a comprehensive list of markers for identifying major cell populations in the head kidney with significant immune relevance.
MeSH term(s)	Animals ; Salmo salar/genetics ; Gene Expression Regulation ; Head Kidney ; Endothelial Cells ; Gene Expression Profiling/veterinary ; Transcriptome ; RNA, Small Nuclear ; Mammals
Chemical Substances	RNA, Small Nuclear
Language	English
Publishing date	2024-01-04
Publishing country	England
Document type	Journal Article
ZDB-ID	1067738-0
ISSN	1095-9947 ; 1050-4648
ISSN (online)	1095-9947
ISSN	1050-4648
DOI	10.1016/j.fsi.2024.109357
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Article ; Online: Cell atlas of the Atlantic salmon spleen reveals immune cell heterogeneity and cell-specific responses to bacterial infection.

Sun, Jianxuan / Ruiz Daniels, Rose / Balic, Adam / Andresen, Adriana M S / Bjørgen, Håvard / Dobie, Ross / Henderson, Neil C / Koppang, Erling Olaf / Martin, Samuel A M / Fosse, Johanna Hol / Taylor, Richard S / Macqueen, Daniel J

Fish & shellfish immunology

2024 Volume 145, Page(s) 109358

Abstract: The spleen is a conserved secondary lymphoid organ that emerged in parallel to adaptive immunity in early jawed vertebrates. Recent studies have applied single cell transcriptomics to reveal the cellular composition of spleen in several species, ... ...

Abstract	The spleen is a conserved secondary lymphoid organ that emerged in parallel to adaptive immunity in early jawed vertebrates. Recent studies have applied single cell transcriptomics to reveal the cellular composition of spleen in several species, cataloguing diverse immune cell types and subpopulations. In this study, 51,119 spleen nuclei transcriptomes were comprehensively investigated in the commercially important teleost Atlantic salmon (Salmo salar L.), contrasting control animals with those challenged with the bacterial pathogen Aeromonas salmonicida. We identified clusters of nuclei representing the expected major cell types, namely T cells, B cells, natural killer-like cells, granulocytes, mononuclear phagocytes, endothelial cells, mesenchymal cells, erythrocytes and thrombocytes. We discovered heterogeneity within several immune lineages, providing evidence for resident macrophages and melanomacrophages, infiltrating monocytes, several candidate dendritic cell subpopulations, and B cells at distinct stages of differentiation, including plasma cells and an igt + subset. We provide evidence for twelve candidate T cell subsets, including cd4+ T helper and regulatory T cells, one cd8+ subset, three γδT subsets, and populations double negative for cd4 and cd8. The number of genes showing differential expression during the early stages of Aeromonas infection was highly variable across immune cell types, with the largest changes observed in macrophages and infiltrating monocytes, followed by resting mature B cells. Our analysis provides evidence for a local inflammatory response to infection alongside B cell maturation in the spleen, and upregulation of ccr9 genes in igt + B cells, T helper and cd8+ cells, and monocytes, consistent with the recruitment of immune cell populations to the gut to deal with Aeromonas infection. Overall, this study provides a new cell-resolved perspective of the immune actions of Atlantic salmon spleen, highlighting extensive heterogeneity hidden to bulk transcriptomics. We further provide a large catalogue of cell-specific marker genes that can be leveraged to further explore the function and structural organization of the salmonid immune system.
MeSH term(s)	Animals ; Spleen ; Salmo salar ; Fish Diseases ; Endothelial Cells ; Bacterial Infections
Language	English
Publishing date	2024-01-03
Publishing country	England
Document type	Journal Article
ZDB-ID	1067738-0
ISSN	1095-9947 ; 1050-4648
ISSN (online)	1095-9947
ISSN	1050-4648
DOI	10.1016/j.fsi.2024.109358
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