Profile of whole blood gene expression following immune stimulation in a wild passerine

Gene expression provides mechanistic insights into a viral disease in seabirds

Wild animals are exposed to a variety of anthropogenic stressors that may result in loss of physiological homeostasis. One main consequence of this stress exposure is the increased vulnerability to pathogens. We addressed the hypothesis that energetic unbalance and alterations of immune effectors are key proximate mechanisms underlying this vulnerability, by quantifying the gene expression of magnificent frigatebird Fregata magnificens chicks affected by a highly lethal viral disease, whose appearance is favoured by food limitation in this species. A comparison between chicks with and without visible clinical signs of the disease using strict threshold of significance (p-value adjusted<0.05 and log2 fold-change above 1 or below -1) revealed 86 upregulated and 9 downregulated genes in sick chicks. The main differentially expressed genes with several fold difference between healthy and sick chicks were linked to biotic and external stimuli, inflammation and antifungal/antibacterial activity, signaling, and hydrolase activity. We further followed the chicks for several weeks, to identify chicks that became sick over the course of the study, to assess how the gene expression profile of chicks may predict the response to the disease. A comparison between chicks that remained always healthy and chicks that showed the appearance of visible clinical signs of the disease revealed 4 upregulated and 8 downregulated genes in chicks that became sick. The main differentially expressed genes with several fold difference between the two phenotypes were linked to cell development and differentiation, metabolism, and immunity. The results of our study suggest that alterations of the energetic machinery and of specific immune effectors (e.g. toll-like receptor, tetraspanins) underlie the impact of a viral disease on a free-living vertebrate. Our study contributes to a more comprehensive understanding of the host-pathogen interaction in wild animals and the physiological pathways involved, and provides insights for effective wildlife disease monitoring and management strategies.

Subclinical peripheral inflammation has systemic effects impacting central nervous system proteome in budgerigars

Regulation of neuroimmune interactions varies across avian species. Little is presently known about the interplay between periphery and central nervous system (CNS) in parrots, birds sensitive to neuroinflammation. Here we investigated the systemic and CNS responses to dextran sulphate sodium (DSS)- and lipopolysaccharide (LPS)-induced subclinical acute peripheral inflammation in budgerigar (Melopsittacus undulatus). Three experimental treatment groups differing in DSS and LPS stimulation were compared to controls. Individuals treated with DSS showed significant histological intestinal damage. Through quantitative proteomics we described changes in plasma (PL) and cerebrospinal fluid (CSF) composition. In total, we identified 180 proteins in PL and 978 proteins in CSF, with moderate co-structure between the proteomes. Between treatments we detected differences in immune, coagulation and metabolic pathways. Proteomic variation was associated with the levels of pro-inflammatory cytokine mRNA expression in intestine and brain. Our findings shed light on systemic impacts of peripheral low-grade inflammation in birds.

Ecoimmunology in the field: Measuring multiple dimensions of immune function with minimally invasive, field-adapted techniques

OBJECTIVE

Immune function is multifaceted and characterizations based on single biomarkers may be uninformative or misleading, particularly when considered across ecological contexts. However, measuring the many facets of immunity in the field can be challenging, since many measures cannot be obtained on-site, necessitating sample preservation and transport. Here we assess state-of-the-art methods for measuring immunity, focusing on measures that require a minimal blood sample obtained from a finger prick, which can be: (1) dried on filter paper, (2) frozen in liquid nitrogen, or (3) stabilized with chemical reagents.

RESULTS

We review immune measures that can be obtained from point-of-care devices or from immunoassays of dried blood spots (DBSs), field methods for flow cytometry, the use of RNA or DNA sequencing and quantification, and the application of immune activation assays under field conditions.

CONCLUSIONS

Stable protein products, such as immunoglobulins and C-reactive protein are reliably measured in DBSs. Because less stable proteins, such as cytokines, may be problematic to measure even in fresh blood, mRNA from stabilized blood may provide a cleaner measure of cytokine and broader immune-related gene expression. Gene methylation assays or mRNA sequencing also allow for the quantification of many other parameters, including the inference of leukocyte subsets, though with less accuracy than with flow cytometry. Combining these techniques provides an improvement over single-marker studies, allowing for a more nuanced understanding of how social and ecological variables are linked to immune measures and disease risk in diverse populations and settings.

Health monitoring in birds using bio-loggers and whole blood transcriptomics

Monitoring and early detection of emerging infectious diseases in wild animals is of crucial global importance, yet reliable ways to measure immune status and responses are lacking for animals in the wild. Here we assess the usefulness of bio-loggers for detecting disease outbreaks in free-living birds and confirm detailed responses using leukocyte composition and large-scale transcriptomics. We simulated natural infections by viral and bacterial pathogens in captive mallards (Anas platyrhynchos), an important natural vector for avian influenza virus. We show that body temperature, heart rate and leukocyte composition change reliably during an acute phase immune response. Using genome-wide gene expression profiling of whole blood across time points we confirm that immunostimulants activate pathogen-specific gene regulatory networks. By reporting immune response related changes in physiological and behavioural traits that can be studied in free-ranging populations, we provide baseline information with importance to the global monitoring of zoonotic diseases.

Blood Transcriptomics of Turbot Scophthalmus maximus: A Tool for Health Monitoring and Disease Studies

Simple Summary

The analysis of blood gene expression is emerging as a relevant source of information about the health status of an organism. While these investigations are increasingly performed in human and terrestrial animals, their potential is still underexplored in fish pathology. The aim of this work was to analyze the blood transcriptional profile of a commercially important flatfish species, turbot (Scophthalmus maximus), in healthy and diseased specimens. The analysis of the most expressed genes in healthy fish indicated that turbot red blood cells have important immunological functions. In diseased fish, parasitized by a myxozoan, the blood analysis reflected a broad inhibition of the immune response followed by intense inflammatory activation in heavy infections. The results showed that turbot response appears delayed, dysregulated and ineffective in stopping the infection. Particularly, a proper development of the adaptive immune response was lacking. This study points out that blood gene expression profiling is a reliable tool for health monitoring, as well as to advance in the knowledge of fish immunity and diseases.

Abstract

Blood transcriptomics is emerging as a relevant tool to monitor the status of the immune system and assist in diagnosis, prognosis, treatment and pathogenesis studies of diseases. In fish pathology, the potential of transcriptome profiling of blood is still poorly explored. Here, RNA sequencing was applied to analyze the blood transcriptional profile of turbot (Scophthalmus maximus), the most important farmed flatfish. The study was conducted in healthy specimens and specimens parasitized by the myxozoan Enteromyxum scophthalmi, which causes one of the most devastating diseases in turbot aquaculture. The blood of healthy turbot showed a transcriptomic profile mainly related to erythrocyte gas transportation function, but also to antigen processing and presentation. In moderately infected turbot, the blood reflected a broad inhibition of the immune response. Particularly, down-regulation of the B cell receptor signaling pathway was shared with heavily parasitized fish, which showed larger transcriptomic changes, including the activation of the inflammatory response. Turbot response to enteromyxosis proved to be delayed, dysregulated and ineffective in stopping the infection. The study evinces that blood transcriptomics can contribute to a better understanding of the teleost immune system and serve as a reliable tool to investigate the physiopathological status of fish.

Differentially Expressed Gene Patterns in Ascarid-Infected Chickens of Higher- or Lower-Performing Genotypes

Simple Summary

Nematode infections may increase mortality and welfare problems in laying hens. The two ascarid worms, Ascaridia galli and Heterakis gallinarum, are highly prevalent in laying hens kept in non-cage housing systems worldwide. The ability of a host to expel pathogens is a component of resistance to diseases. The molecular basis of differences between different host animals in their efficiency to expel worms is, however, not well understood. Therefore, we performed a detailed analysis of differentially expressed genes (DEGs) in two chicken genotypes (Lohmann Brown Plus (LB), Lohmann Dual (LD)), each with a lower or higher infection intensity level of A. galli and H. gallinarum. Our data showed significant upregulation of Guanylate Binding Protein 7 (GBP7) in LD hens. Gene ontology analysis revealed higher transcriptome activity related to “response to external stimulus” in LB hens, implying a higher stress response in this genotype. In contrast, LD hens showed higher transcriptomic expression of genes associated with a higher tolerance to infections.

Abstract

Here, we describe the first transcriptomic investigation of the peripheral blood of chickens exposed to Ascaridia galli and Heterakis gallinarum infections. We investigated differentially expressed gene (DEG) patterns in two chicken genotypes with either a higher (Lohmann Brown Plus, LB) or lower (Lohmann Dual, LD) laying performance level. The hens were experimentally coinfected with A. galli and H. gallinarum, and their worm burdens and infection parameters were determined six weeks post infection. Based on most representative infection parameters, the hens were clustered into lower- and higher-infection intensity classes. We identified a total of 78 DEGs contributing to infection-related phenotypic variation in the two genotypes. Our data showed significant upregulation of Guanylate Binding Protein 7 (GBP7) in LD hens, making it a promising candidate for tolerance to ascarid infections in chickens. Gene ontology analysis revealed higher transcriptome activity related to biological processes such as “response to external stimulus” in LB hens, implying a higher stress response in this genotype. In contrast, LD hens showed higher transcriptomic expression of genes related to ontology classes that are possibly associated with a higher tolerance to infections. These findings may help explain why lower-performing genotypes (i.e., LD) are less sensitive to infections in terms of maintaining their performance.

Increased glucocorticoid concentrations in early life cause mitochondrial inefficiency and short telomeres

Telomeres are DNA structures that protect chromosome ends. However, telomeres shorten during cell replication and at critically low lengths can reduce cell replicative potential, induce cell senescence and decrease fitness. Stress exposure, which elevates glucocorticoid hormone concentrations, can exacerbate telomere attrition. This phenomenon has been attributed to increased oxidative stress generated by glucocorticoids ('oxidative stress hypothesis'). We recently suggested that glucocorticoids could increase telomere attrition during stressful periods by reducing the resources available for telomere maintenance through changes in the metabolic machinery ('metabolic telomere attrition hypothesis'). Here, we tested whether experimental increases in glucocorticoid levels affected telomere length and mitochondrial function in wild great tit (Parus major) nestlings during the energy-demanding early growth period. We monitored resulting corticosterone (Cort) concentrations in plasma and red blood cells, telomere lengths and mitochondrial metabolism (metabolic rate, proton leak, oxidative phosphorylation, maximal mitochondrial capacity and mitochondrial inefficiency). We assessed oxidative damage caused by reactive oxygen species (ROS) metabolites as well as the total non-enzymatic antioxidant protection in plasma. Compared with control nestlings, Cort-nestlings had higher baseline corticosterone, shorter telomeres and higher mitochondrial metabolic rate. Importantly, Cort-nestlings showed increased mitochondrial proton leak, leading to a decreased ATP production efficiency. Treatment groups did not differ in oxidative damage or antioxidants. Hence, glucocorticoid-induced telomere attrition is associated with changes in mitochondrial metabolism, but not with ROS production. These findings support the hypothesis that shortening of telomere length during stressful periods is mediated by glucocorticoids through metabolic rearrangements.

Blood transcriptome resources of chinstrap (Pygoscelis antarcticus) and gentoo (Pygoscelis papua) penguins from the South Shetland Islands, Antarctica

The chinstrap (Pygoscelis antarcticus) and gentoo (P. papua) penguins are distributed throughout Antarctica and the sub-Antarctic islands. In this study, high-quality de novo assemblies of blood transcriptomes from these penguins were generated using the Illumina MiSeq platform. A total of 22.2 and 21.8 raw reads were obtained from chinstrap and gentoo penguins, respectively. These reads were assembled using the Oases assembly platform and resulted in 26,036 and 21,854 contigs with N50 values of 929 and 933 base pairs, respectively. Functional gene annotations through pathway analyses of the Gene Ontology, EuKaryotic Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were performed for each blood transcriptome, resulting in a similar compositional order between the two transcriptomes. Ortholog comparisons with previously published transcriptomes from the Adélie (P. adeliae) and emperor (Aptenodytes forsteri) penguins revealed that a high proportion of the four penguins’ transcriptomes had significant sequence homology. Because blood and tissues of penguins have been used to monitor pollution in Antarctica, immune parameters in blood could be important indicators for understanding the health status of penguins and other Antarctic animals. In the blood transcriptomes, KEGG analyses detected many essential genes involved in the major innate immunity pathways, which are key metabolic pathways for maintaining homeostasis against exogenous infections or toxins. Blood transcriptome studies such as this may be useful for checking the immune and health status of penguins without sacrifice.

RNA-seq analysis of the kidneys of broiler chickens fed diets containing different concentrations of calcium

Calcium (Ca) is required for normal growth and is involved in cellular physiology, signal transduction, and bone mineralization. In humans, inadequate Ca intake causes hypocalcaemia, and excessive Ca intake causes hypercalcemia. In chicken, Ca is also required for body weight gain and eggshell formation. However, transcriptomic responses to low/high Ca intake, and mechanisms affecting body weight have not been explored. In this study, we performed comparative RNA sequencing (RNA-seq) using the kidney of broiler chickens fed diets containing 0.8, 1.0, and 1.2% Ca. Annotation of RNA-seq data revealed a significant number of differentially expressed genes (DEGs) in the kidney via pairwise comparison using Cufflinks and edgeR. Using edgeR, we identified 12 DEGs; seven overlapped with those found by cufflinks. Seven DEGs were validated by real-time quantitative-PCR (qRT-PCR) in Ca-supplemented kidneys, and the results correlated with the RNA-seq data. DEGs identified by cufflinks/edgeR were subjected to pathway enrichment, protein/protein interaction, and co-occurrence analyses to determine their involvement in disease. The National Research Council (NRC) recommended Ca intake for 21-day post-hatch broilers is about 1.0%. Our findings suggest that higher-than-recommended Ca intake (1.2%) could reduce body weight gain in broilers, and that affected DEGs are related to stress-induced diseases, such as hypertension.

De Novo Assembly of the Liver Transcriptome of the European Starling, Sturnus vulgaris

The European starling, Sturnus vulgaris, is a prolific and worldwide invasive species that also has served as an important model for avian ecological and invasion research. Although the genome sequence recently has become available, no transcriptome data have been published for this species. Here, we have sequenced and assembled the S. vulgaris liver transcriptome, which will provide a foundational resource for further annotation and validation of the draft genome. Moreover, it will be important for ecological and evolutionary studies investigating the genetic factors underlying rapid evolution and invasion success in this global invader.

Transcriptomes of whole blood and PBMC in chickens

Global transcriptome analysis of chicken whole blood to discover biomarkers of different phenotypes or physiological disorders has never been investigated so far. Whole blood provides significant advantages, allowing large scale and non-invasive sampling. However, generation of gene expression data from the blood of non-mammalian species remains a challenge, notably due to the nucleated red blood cells, hindering the use of well-established protocols. The aim of this study was to analyze the relevance of using whole blood cells (WB) to find biomarkers, instead of Peripheral Blood Mononuclear Cells (PBMC), usually chosen for immune challenges. RNA sources from WB and PBMC was characterized by microarray analysis. Our results show that the quality and quantity of RNA obtained from WB was suitable for further analyses, although the quality was lower than that from PBMC. The transcriptome profiling comparison revealed that the majority of genes were expressed in both WB and PBMC. Hemoglobin subunits were the major transcripts in WB, whereas the most enriched biological process was related to protein catabolic process. Most of the over-represented transcripts in PBMC were implicated in functions specific to thrombocytes, like coagulation and platelet activation, probably due to the large proportion of this nucleated cell type in chicken PBMC. Functions related to B and T cells and to other immune functions were also enriched in the PBMC subset. We conclude that WB is more suitable for large scale immunity oriented studies and other biological processes that have been poorly investigated so far.

Assessing models of speciation under different biogeographic scenarios; an empirical study using multi-locus and RNA-seq analyses

Evolutionary biology often seeks to decipher the drivers of speciation, and much debate persists over the relative importance of isolation and gene flow in the formation of new species. Genetic studies of closely related species can assess if gene flow was present during speciation, because signatures of past introgression often persist in the genome. We test hypotheses on which mechanisms of speciation drove diversity among three distinct lineages of desert tortoise in the genus Gopherus. These lineages offer a powerful system to study speciation, because different biogeographic patterns (physical vs. ecological segregation) are observed at opposing ends of their distributions. We use 82 samples collected from 38 sites, representing the entire species' distribution and generate sequence data for mtDNA and four nuclear loci. A multilocus phylogenetic analysis in *BEAST estimates the species tree. RNA‐seq data yield 20,126 synonymous variants from 7665 contigs from two individuals of each of the three lineages. Analyses of these data using the demographic inference package ∂a∂i serve to test the null hypothesis of no gene flow during divergence. The best‐fit demographic model for the three taxa is concordant with the *BEAST species tree, and the ∂a∂i analysis does not indicate gene flow among any of the three lineages during their divergence. These analyses suggest that divergence among the lineages occurred in the absence of gene flow and in this scenario the genetic signature of ecological isolation (parapatric model) cannot be differentiated from geographic isolation (allopatric model).

Transcriptomic Characterization of Innate and Acquired Immune Responses in Red-Legged Partridges (Alectoris rufa): A Resource for Immunoecology and Robustness Selection

Present and future challenges for wild partridge populations include the resistance against possible disease transmission after restocking with captive-reared individuals, and the need to cope with the stress prompted by new dynamic and challenging scenarios. Selection of individuals with the best immune ability may be a good strategy to improve general immunity, and hence adaptation to stress. In this study, non-infectious challenges with phytohemagglutinin (PHA) and sheep red blood cells allowed the classification of red-legged partridges (Alectoris rufa) according to their overall immune responses (IR). Skin from the area of injection of PHA and spleen, both from animals showing extreme high and low IR, were selected to investigate the transcriptional profiles underlying the different ability to cope with pathogens and external aggressions. RNA-seq yielded 97 million raw reads from eight sequencing libraries and approximately 84% of the processed reads were mapped to the reference chicken genome. Differential expression analysis identified 1488 up- and 107 down-regulated loci in individuals with high IR versus low IR. Partridges displaying higher innate IR show an enhanced activation of host defence gene pathways complemented with a tightly controlled desensitization that facilitates the return to cellular homeostasis. These findings indicate that the immune system ability to respond to aggressions (either diseases or stress produced by environmental changes) involves extensive transcriptional and post-transcriptional regulations, and expand our understanding on the molecular mechanisms of the avian immune system, opening the possibility of improving disease resistance or robustness using genome assisted selection (GAS) approaches for increased IR in partridges by using genes such as AVN or BF2 as markers. This study provides the first transcriptome sequencing data of the Alectoris genus, a resource for molecular ecology that enables integration of genomic tools in further studies.