Selection of reference genes for RT-qPCR studies in blood of beluga whales (Delphinapterus leucas)

A Field-Deployable Insulated Isothermal PCR (iiPCR) for the Global Surveillance of Toxoplasma gondii Infection in Cetaceans

Simple Summary

Since high trophic levels marine mammal species share the coastal environments and diets with humans, cetaceans provide an indication of contaminant bioaccumulation in humans and may serve as sentinels for public health problems. Parasite monitoring in marine sentinels can assist in evaluating the quality of the aquatic ecosystem’s health. T. gondii infection in cetaceans is an indicator of land-to-sea coastal pollution. Although T. gondii infection cases in cetaceans have been reported in several countries, an information gap still exists in some areas. The present study employs a portable insulated isothermal PCR (iiPCR) with an automatic extraction device as a rapid, affordable, user-friendly, and field-deployable platform to rapidly detect nucleic acid of T. gondii in stranded cetaceans. The platform utilizes duplex iiPCR designed to simultaneously detect T. gondii and a housekeeping gene of cetacean on the samples, which can prevent the false-negative results of pathogen detection and improve the accuracy of surveillance. This study would contribute to improving the environment through the warning of the sentinel animals and building new strategies by detecting the occurrence of land-based biological pollution.

Abstract

Toxoplasmosis is a zoonotic disease with veterinary and public health importance worldwide. Toxoplasma gondii infection in cetaceans is an indicator of land-to-sea oocyst pollution. However, there is a critical knowledge gap within the distribution of the T. gondii infection in cetaceans. To facilitate the global surveillance of this important zoonotic pathogen, we developed a field-deployable duplex insulated isothermal PCR (iiPCR) with automated magnetic bead-based DNA extraction for the on-site detection of T. gondii in stranded cetaceans. It targets the B1 gene of T. gondii combined with β2-microglobulin (B2M) gene of cetaceans as an internal control. Compared with the conventional qPCR assay, B1/B2M duplex iiPCR assay showed comparable sensitivity (21~86 bradyzoites in 25 mg of tissue) to detect spike-in standard of T. gondii DNA in cerebrum, cerebellum, skeletal muscle and myocardium tissues. Moreover, the overall agreement between the duplex iiPCR and qPCR was in almost perfect agreement (92%; 95% CI: 0.78–0.90; κ = 0.84) in detecting a synthetic spike-in standards. The B1/B2M iiPCR assay coupled with a field-deployable system provides a prompt (~1.5 h), feasible, highly sensitive and specific on-site diagnostic tool for T. gondii in stranded cetaceans. This platform provides one approach to evaluating aquatic ecosystem health and developing early warnings about negative impacts on humans and marine animals.

An example of DNA methylation as a means to quantify stress in wildlife using killer whales

The cumulative effects of non-lethal stressors on the health of biodiversity are a primary concern for conservation, yet difficulties remain regarding their quantification. In mammals, many stressors are processed through a common stress-response pathway, and therefore epigenetic changes in genes of this pathway may provide a powerful tool for quantifying cumulative effects. As a preliminary assessment of this approach, we investigated epigenetic manifestations of stress in two killer whale populations with different levels of exposure to anthropogenic stressors. We used bisulfite amplicon sequencing to compare patterns of DNA methylation at 25 CpG sites found in three genes involved in stress response and identified large differences in the level of methylation at two sites consistent with differential stress exposure between Northern and Southern Resident killer whale populations. DNA methylation patterns could therefore represent a useful method to assess the cumulative effects of non-lethal stressors in wildlife.

Cytokine RT-qPCR and ddPCR for immunological investigations of the endangered Australian sea lion (Neophoca cinerea) and other mammals

Measurement of cytokine gene expression by reverse transcription quantitative polymerase chain reaction (RT-qPCR) is used widely to assess the immune system of animals and to identify biomarkers of disease, but its application is limited in wildlife species due to a lack of species-specific reagents. The free-ranging endangered Australian sea lion (Neophoca cinerea) experiences significant clinical disease and high pup mortality due to intestinal hookworm infection. Developing immunological tools specific to the species will aid in the assessment of drivers of disease and its impact in population demographics. This study describes the development and validation of cross-reactive RT-qPCR assays to measure five important cytokines involved in innate and Th1/Th2 responses (IL-6, TNFα, IFNγ, IL-4 and IL-10) in unstimulated blood samples from a range of different mammalian species including the Australian sea lion. All RT-qPCR assays efficiencies ranged between 87% (Ovis aries TNFα) and 111% (Bos taurus IL-10) and had strong linearity (R²). IL-4 and IFNγ gene expression for N. cinerea fell below the dynamic range (and therefore quantifiable limits) of RT-qPCR assays but were able to be quantified using the novel droplet digital PCR (ddPCR). This study delivers new immunological tools for eco-immunologists studying cytokine gene expression in wildlife species and is to our knowledge, the first cytokine ddPCR approach to be reported in a pinniped species.

IMMUNOMEDIATOR GENE TRANSCRIPTION PROFILING IN BELUGA WHALE (DELPHINAPTERUS LEUCAS) CLINICAL CASES

There is an unmet need for specific diagnostics of immune perturbations and inflammation in beluga whale (Delphinapterus leucas) clinical care. Quantitative real-time polymerase chain reaction (qPCR) has been used to measure immunomediator gene transcription in beluga whales. The study hypothesis was that a qPCR-based immunomediator assay would supplement routine clinical data with specific and sensitive information on immune status. Two beluga whale clinical cases provided an opportunity to test this hypothesis: a whale with a skin laceration and a whale with gastrointestinal inflammation. Mitogen-stimulated immunomediator gene transcription (MSIGT) was compared between the cases and healthy contact whales. In both case studies, mitogens increased transcription of IL1B, PTGS2 (Cox-2), TNF, HIF1A, and IL2 but decreased IL10 transcription in peripheral blood mononuclear cells (PBMC) from the abnormal whale over the control. Correlations were identified between most immunomediators tested and one or more standard blood clinical values. Considering all 15 immunomediators tested, the whale with gastrointestinal inflammation had a more unique MSIGT signature than the whale with a laceration. These results support further elucidation of beluga whale PBMC cytokine profiles for use as immune biomarkers.

Associations between organohalogen exposure and thyroid- and steroid-related gene responses in St. Lawrence Estuary belugas and minke whales

Elevated concentrations of persistent organic pollutants (POPs) and emerging halogenated flame retardants (HFRs) have been reported in tissues of the endangered St. Lawrence Estuary (Canada) beluga population as well as in minke whales visiting that same feeding area. This study examined the linkages between blubber concentrations of POPs and emerging HFRs, and transcription in skin of genes involved in the regulation of thyroid and steroid axes in belugas and minke whales from the St. Lawrence Estuary. In belugas, concentrations of PCBs, OCs and hexabromobenzene (HBB) were positively correlated with the transcription of thyroid- and/or steroid-related genes, while Dec-604 CB concentrations were negatively associated with the transcription of glucocorticoid and thyroid genes. In minke whales, PBDE concentrations changed positively with Esrβ transcript levels and HBB concentrations negatively with Nr3c1 transcripts. Present results suggest that several biological functions including reproduction and energetic metabolism may represent potential targets for organohalogens in these whales.

Transcriptome profiling based on protein-protein interaction networks provides a core set of genes for understanding blood immune response mechanisms against Edwardsiella tarda infection in Japanese flounder (Paralichthys olivaceus)

Marine organisms are commonly under threat from various pathogens. Edwardsiella tarda is one of the fish pathogens that can infect both cultured and wild fish species. E. tarda can also infect other vertebrates, including amphibians, reptiles, and mammals. Bacteremia caused by E. tarda can be a fatal disease in humans. Blood acts as a pipeline for the fish immune system. Generating blood transcriptomic resources from fish challenged by E. tarda is crucial for understanding molecular mechanisms underlying blood immune response process. In this study, we performed transcriptome-wide gene expression profiling of Japanese flounder (Paralichthys olivaceus) challenged by 8 and 48 h E. tarda stress. An average of 37 million clean reads per library was obtained, and approximately 85.6% of these reads were successfully mapped to the reference genome. In addition, 808 and 1265 differential expression genes (DEGs) were found at 8 and 48 h post-injection, respectively. Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted to search immune-related DEGs. A protein-protein interaction network was constructed to obtain the interaction relationship of immune genes during pathogens stress. Based on KEGG and protein association networks analysis, 30 hub genes were discovered and validated by quantitative RT-PCR. This study represents the first transcriptome analysis based on protein-protein interaction networks in fish and provides us with valuable gene resources for the research of fish blood immunity, which can significantly assist us to further understand the molecular mechanisms of humans and other vertebrates against E. tarda.

A probe-based qRT-PCR method to profile immunological gene expression in blood of captive beluga whales (Delphinapterus leucas)

Cytokines are fundamental for a functioning immune system, and thus potentially serve as important indicators of animal health. Quantitation of mRNA using quantitative reverse transcription polymerase chain reaction (qRT-PCR) is an established immunological technique. It is particularly suitable for detecting the expression of proteins against which monoclonal antibodies are not available. In this study, we developed a probe-based quantitative gene expression assay for immunological assessment of captive beluga whales (Delphinapterus leucas) that is one of the most common cetacean species on display in aquariums worldwide. Six immunologically relevant genes (IL-2Rα, -4, -10, -12, TNFα, and IFNγ) were selected for analysis, and two validated housekeeping genes (PGK1 and RPL4) with stable expression were used as reference genes. Sixteen blood samples were obtained from four animals with different health conditions and stored in RNAlater™ solution. These samples were used for RNA extraction followed by qRT-PCR analysis. Analysis of gene transcripts was performed by relative quantitation using the comparative Cq method with the integration of amplification efficiency and two reference genes. The expression levels of each gene in the samples from clinically healthy animals were normally distributed. Transcript outliers for IL-2Rα, IL-4, IL-12, TNFα, and IFNγ were noticed in four samples collected from two clinically unhealthy animals. This assay has the potential to identify immune system deviation from normal state, which is caused by health problems. Furthermore, knowing the immune status of captive cetaceans could help both trainers and veterinarians in implementing preventive approaches prior to disease onset.

Optimal reference genes for RT-qPCR normalization in the newborn

It is difficult to identify reliable reference genes for transcriptomic analyses in biofluids such as saliva. This situation is particularly relevant for the newborn population, where rapid development is associated with dynamic changes in gene expression. Real-time gene expression monitoring holds great promise for elucidating disrupted pathways that result in morbidities unique to this population, such as retinopathy of prematurity, but its impact depends on identifying stable and consistently expressed genes across a wide range of gestational ages. We extracted total RNA from 400 neonatal saliva samples (postconceptional ages: 32 5/7 to 48 2/7 weeks), converted it to cDNA, and pre-amplified and analyzed it by qPCR for three commonly used reference genes, ACTB, GAPDH, and YWHAZ. Relative quantification was determined using the Δ Ct method. Data were analyzed as a whole and also stratified by age and sex. Descriptive statistics and homogeneity of variance were performed to identify optimal reference genes. Data analyzed from all ages and both sexes showed significant expression variation for ACTB, while GAPDH and YWHAZ showed greater stability. Male infants exhibited increased expression variation compared to females for ACTB, but neither GAPDH nor YWHAZ showed significant variance for either sex. We suggest that ACTB is an unreliable reference gene for the newborn population. Males showed significantly more variation in ACTB expression compared to females, which suggests a sex-specific developmental role for this biomarker. By contrast, GAPDH and YWHAZ were less variable and therefore preferable for use in neonates. Our findings may improve the use of reference genes for the RT-qPCR platform in the newborn over a wide range of gestational ages, thereby minimizing the likelihood of erroneous interpretation of gene expression during rapid growth, development, and differentiation.