Profiling the rainbow trout hepatic miRNAome under diet-induced hyperglycemia

The dynamic transcriptomic response of the goldfish brain under chronic hypoxia

Oxygen is essential to fuel aerobic metabolism. Some species evolved mechanisms to tolerate periods of severe hypoxia and even anoxia in their environment. Among them, goldfish (Carassius auratus) are unique, in that they do not enter a comatose state under severely hypoxic conditions. There is thus significant interest in the field of comparative physiology to uncover the mechanistic basis underlying hypoxia tolerance in goldfish, with a particular focus on the brain. Taking advantage of the recently published and annotated goldfish genome, we profile the transcriptomic response of the goldfish brain under normoxic (21 kPa oxygen saturation) and, following gradual reduction, constant hypoxic conditions after 1 and 4 weeks (2.1 kPa oxygen saturation). In addition to analyzing differentially expressed protein-coding genes and enriched pathways, we also profile differentially expressed microRNAs (miRs). Using in silico approaches, we identify possible miR-mRNA relationships. Differentially expressed transcripts compared to normoxia were either common to both timepoints of hypoxia exposure (n = 174 mRNAs; n = 6 miRs), or exclusive to 1-week (n = 441 mRNAs; n = 23 miRs) or 4-week hypoxia exposure (n = 491 mRNAs; n = 34 miRs). Under chronic hypoxia, an increasing number of transcripts, including those of paralogous genes, was downregulated over time, suggesting a decrease in transcription. GO-terms related to the vascular system, oxidative stress, stress signalling, oxidoreductase activity, nucleotide- and intermediary metabolism, and mRNA posttranscriptional regulation were found to be enriched under chronic hypoxia. Known 'hypoxamiRs', such as miR-210-3p/5p, and miRs such as miR-29b-3p likely contribute to posttranscriptional regulation of these pathways under chronic hypoxia in the goldfish brain.

Exploring transcriptional and post-transcriptional epigenetic regulation of crf and 11βhsd2 in rainbow trout brain during chronic social stress

Using dominance hierarchies in juvenile rainbow trout (Oncorhynchus mykiss) as a model of chronic social stress in fish, we explored whether epigenetic transcriptional and post-transcriptional mechanisms are involved in the gene expression of corticotropin-releasing factor (crf) and 11β-hydroxysteroid dehydrogenase (11βhsd2), key factors involved in the regulation of the endocrine stress axis response. In juvenile rainbow trout pairs, subordinate individuals display sustained elevation of circulating cortisol concentrations. Cortisol production is controlled by the hypothalamic-pituitary-interrenal (HPI) axis in fish and initiated by CRF release from the preoptic area (POA). Given that crf is modulated during chronic social stress, and that such stress has been implicated in the epigenetic regulation of crf in other taxa, we probed a role for epigenetic regulation of crf transcript abundance in chronically stressed rainbow trout. We also investigated the regulation of the cortisol-metabolising enzyme 11βhsd2 in the POA, which is upregulated in subordinates. The potential involvement of DNA methylation and microRNAs (miRNAs) in the regulation of crf transcript abundance was investigated during social stress in the POA of fish, as was the potential involvement of miRNAs in 11βhsd2 regulation. Although transcript abundances of crf were elevated in subordinate fish after 4 days, DNA methylation profiles within putative promoter sequences upstream of the crf gene were not significantly affected by chronic stress. An inverse relationship between crf and its predicted posttranscriptional regulator miR-103a-3p in the POA suggests that miRNAs may be involved in mediating the effects of chronic social stress on key components of the endocrine stress axis.

Red Vetchling (Lathyrus cicera L.), a Promising Crop for the Sustainable Replacement of Soybean Meal and Reducing the Carbon Footprint of European Aquafeeds

In fish diets, soybean meal (SBM) is still positioned as the most widely used alternative to replace fishmeal. Red vetchling (Lathyrus cicera), a crop locally produced in Europe, is here evaluated as a substitute for SBM. Rainbow trout (Oncorhynchus mykiss) juveniles (10.34 ± 0.04 g) were fed for 90 days. Six experimental diets replacing the SBM content at 0, 8, 16, 33, 66, and 100% (Named Control, T8, T16, T33, T66, and T100) were tested. Growth performance and fish fillet amino acid composition were only significantly reduced in fish fed the T100 diet. Histopathological analysis showed that no major alterations were observed in the intestine, while T100 fish had a higher density of pyknotic nuclei in the hepatocytes than the Control, but similar hepatocyte surface coverage. Finally, postprandial levels of glucose and triglycerides in blood plasma decreased when red vetchling content was increased, but was only not fully restored after 24 h in the case of glucose in T66 and T100 fish. According to these results, red vetchling meal can replace up to 66% of the SBM without a negative effect on fish growth or physiology, representing a good alternative raw material for reducing European aquaculture's dependency on SBM imports and the carbon footprint of aquafeeds.

miRDM-rfGA: Genetic algorithm-based identification of a miRNA set for detecting type 2 diabetes

BACKGROUND

Type 2 diabetes mellitus (T2DM) affects approximately 451 million adults globally. In this study, we identified the optimal combination of marker candidates for detecting T2DM using miRNA-Seq data from 95 samples including T2DM and healthy individuals.

METHODS

We utilized the genetic algorithm (GA) in the discovery of an optimal miRNA biomarker set. We discovered miRNA subsets consisting of three miRNAs for detecting T2DM by random forest-based GA (miRDM-rfGA) as a feature selection algorithm and created six GA parameter settings and three settings using traditional feature selection methods (F-test and Lasso). We then evaluated the prediction performance to detect T2DM in the miRNA subsets derived from each setting.

RESULTS

The miRNA subset in setting 5 using miRDM-rfGA performed the best in detecting T2DM (mean AUROC = 0.92). Target mRNA identification and functional enrichment analysis of the best miRNA subset (hsa-miR-125b-5p, hsa-miR-7-5p, and hsa-let-7b-5p) validated that this combination was involved in T2DM. We also confirmed that the targeted genes were negatively correlated with the clinical variables related to T2DM in the BxD mouse genetic reference population database.

CONCLUSIONS

Using GA in miRNA-Seq data, we identified the optimal miRNA biomarker set for T2DM detection. GA can be a useful tool for biomarker discovery and drug-target identification.

Sequential Activations of ChREBP and SREBP1 Signals Regulate the High-Carbohydrate Diet-Induced Hepatic Lipid Deposition in Gibel Carp (Carassius gibelio)

The present study investigated the sequential regulation signals of high-carbohydrate diet (HCD)-induced hepatic lipid deposition in gibel carp (Carassius gibelio). Two isonitrogenous and isolipidic diets, containing 25% (normal carbohydrate diet, NCD) and 45% (HCD) corn starch, were formulated to feed gibel carp (14.82 ± 0.04 g) for 8 weeks. The experimental fish were sampled at 2^nd, 4^th, 6^th, and 8^th week. In HCD group, the hyperlipidemia and significant hepatic lipid deposition (oil red O area and triglyceride content) was found at 4^th, 6^th, and 8^th week, while the significant hyperglycemia was found at 2^nd, 4^th, and 8^th week, compared to NCD group (P < 0.05). HCD induced hepatic lipid deposition via increased hepatic lipogenesis (acc, fasn, and acly) but not decreased hepatic lipolysis (hsl and cpt1a). When compared with NCD group, HCD significantly elevated the hepatic sterol regulatory element binding proteins 1 (SREBP1) signals (positive hepatocytes and fluorescence intensity) at 4^th, 6^th, and 8^th week (P < 0.05). The hepatic SREBP1 signals increased from 2^nd to 6^th week, but decreased at 8^th week due to substantiated insulin resistance (plasma insulin levels, plasma glucose levels, and P-AKT^Ser473 levels) in HCD group. Importantly, the hepatic carbohydrate response element binding protein (ChREBP) signals (positive hepatocytes, fluorescence intensity, and expression levels) were all significantly elevated by HCD-induced glucose-6-phosphate (G6P) accumulation at 2^nd, 4^th, 6^th, and 8^th week (P < 0.05). Compared to 2^nd and 4^th week, the hepatic ChREBP signals and G6P contents was significantly increased by HCD at 6^th and 8^th week (P < 0.05). The HCD-induced G6P accumulation was caused by the significantly increased expression of hepatic gck, pklr, and glut2 (P < 0.05) but not 6pfk at 4^th, 6^th, and 8^th week, compared to NCD group. These results suggested that the HCD-induced hepatic lipid deposition was mainly promoted by SREBP1 in earlier stage and by ChREBP in later stage for gibel carp. This study revealed the sequential regulation pathways of the conversion from feed carbohydrate to body lipid in fish.

Attenuated glucose uptake promotes catabolic metabolism through activated AMPK signaling and impaired insulin signaling in zebrafish

Glucose metabolism in fish remains a controversial area of research as many fish species are traditionally considered glucose-intolerant. Although energy homeostasis remodeling has been observed in fish with inhibited fatty acid β-oxidation (FAO), the effects and mechanism of the remodeling caused by blocked glucose uptake remain poorly understood. In this study, we blocked glucose uptake by knocking out glut2 in zebrafish. Intriguingly, the complete lethality, found in Glut2-null mice, was not observed in glut2^-/- zebrafish. Approxiamately 30% of glut2^-/- fish survived to adulthood and could reproduce. The maternal zygotic mutant glut2 (MZglut2) fish exhibited growth retardation, decreased blood and tissue glucose levels, and low locomotion activity. The decreased pancreatic β-cell numbers and insulin expression, as well as liver insulin receptor a (insra), fatty acid synthesis (chrebp, srebf1, fasn, fads2, and scd), triglyceride synthesis (dgat1a), and muscle mechanistic target of rapamycin kinase (mtor) of MZglut2 zebrafish, suggest impaired insulin-dependent anabolic metabolism. Upregulated expression of lipolysis (atgl and lpl) and FAO genes (cpt1aa and cpt1ab) in the liver and proteolysis genes (bckdk, glud1b, and murf1a) in muscle were observed in the MZglut2 zebrafish, as well as elevated levels of P-AMPK proteins in both the liver and muscle, indicating enhanced catabolic metabolism associated with AMPK signaling. In addition, decreased amino acids and elevated carnitines of the MZglut2 zebrafish supported the decreased protein and lipid content of the whole fish. In summary, we found that blocked glucose uptake impaired insulin signaling-mediated anabolism via β-cell loss, while AMPK signaling-mediated catabolism was enhanced. These findings reveal the mechanism of energy homeostasis remodeling caused by blocked glucose uptake, which may be a potential strategy for adapting to low glucose levels.

The mammalian insulin antagonist S961 does not exhibit insulin receptor antagonism in rainbow trout in vivo

Due to their reported 'glucose-intolerant' phenotype, rainbow trout have been the focus of comparative studies probing underlying endocrine mechanisms at the organismal, tissue and molecular level. A particular focus has been placed on the investigation of the comparative role of insulin, an important glucoregulatory hormone, and its interaction with macronutrients. A limiting factor in the comparative investigation of insulin is the current lack of reliable assays to quantify circulating mature and thus bioactive insulin. To circumvent this limitation, tissue-specific responsiveness to postprandial or exogenous insulin has been quantified at the level of post-translational modifications of cell signalling proteins. These studies revealed that the insulin responsiveness of these proteins and their post-translational modifications are evolutionarily highly conserved and thus provide useful and quantifiable proxy indices to investigate insulin function in rainbow trout. While the involvement of specific branches of the intracellular insulin signalling pathway (e.g., mTor) in rainbow trout glucoregulation have been successfully probed through pharmacological approaches, it would be useful to have a functionally validated insulin receptor antagonist to characterize the glucoregulatory role of the insulin receptor pathway in its entirety for this species. Here, we report two separate in vivo experiments to test the ability of the mammalian insulin receptor antagonist, S961, to efficiently block insulin signalling in liver and muscle in response to endogenously released insulin and to exogenously infused bovine insulin. We found that, irrespective of the experimental treatment or dose, activation of the insulin pathway in liver and muscle was not inhibited by S961, showing that its antagonistic effect does not extend to rainbow trout.

A cross-species comparative approach to assessing multi- and transgenerational effects of endocrine disrupting chemicals

A wide range of chemicals have been identified as endocrine disrupting chemicals (EDCs) in vertebrate species. Most studies of EDCs have focused on exposure of both male and female adults to these chemicals; however, there is clear evidence that EDCs have dramatic effects when mature or developing gametes are exposed, and consequently are associated with in multigenerational and transgenerational effects. Several publications have reviewed such actions of EDCs in subgroups of species, e.g., fish or rodents. In this review, we take a holistic approach synthesizing knowledge of the effects of EDCs across vertebrate species, including fish, anurans, birds, and mammals, and discuss the potential mechanism(s) mediating such multi- and transgenerational effects. We also propose a series of recommendations aimed at moving the field forward in a structured and coherent manner.

Bacillus amyloliquefaciens ameliorates high-carbohydrate diet-induced metabolic phenotypes by restoration of intestinal acetate-producing bacteria in Nile Tilapia

Poor utilisation efficiency of carbohydrate always leads to metabolic phenotypes in fish. The intestinal microbiota plays an important role in carbohydrate degradation. Whether the intestinal bacteria could alleviate high-carbohydrate diet (HCD)-induced metabolic phenotypes in fish remains unknown. Here, a strain affiliated to Bacillus amyloliquefaciens was isolated from the intestine of Nile tilapia. A basal diet (CON), HCD or HCD supplemented with B. amy SS1 (HCB) was used to feed fish for 10 weeks. The beneficial effects of B. amy SS1 on weight gain and protein accumulation were observed. Fasting glucose and lipid deposition were decreased in the HCB group compared with the HCD group. High-throughput sequencing showed that the abundance of acetate-producing bacteria was increased in the HCB group relative to the HCD group. Gas chromatographic analysis indicated that the concentration of intestinal acetate was increased dramatically in the HCB group compared with that in the HCD group. Glucagon-like peptide-1 was also increased in the intestine and serum of the HCB group. Thus, fish were fed with HCD, HCD supplemented with sodium acetate at 900 mg/kg (HLA), 1800 mg/kg (HMA) or 3600 mg/kg (HHA) diet for 8 weeks, and the HMA and HHA groups mirrored the effects of B. amy SS1. This study revealed that B. amy SS1 could alleviate the metabolic phenotypes caused by HCD by enriching acetate-producing bacteria in fish intestines. Regulating the intestinal microbiota and their metabolites might represent a powerful strategy for fish nutrition modulation and health maintenance in future.

Effects of physical activity on cell-to-cell communication during type 2 diabetes: A focus on miRNA signaling

Type 2 diabetes (TD2) is a progressive disease characterized by hyperglycemia that results from alteration in insulin secretion, insulin resistance, or both. A number of alterations involving different tissues and organs have been reported to the development and the progression of T2D, and more relevantly, through cell-to-cell communication pathways. Recent studies demonstrated that miRNAs are considerably implicated to cell-to-cell communication during T2D. Physical activity (PA) is associated with decreasing risks of developing T2D and acts as insulin-like factor. Cumulative evidence suggests that this effect could be mediated in part through improving insulin sensitivity in T2D and obese patients and modulating miRNAs synthesis and release in healthy patients. Therefore, the practice of PA should ideally be established before the initiation of T2D. This review describes cell-to-cell communications involved in the pathophysiology of T2D during PA.

Meta-analysis of differentially-regulated hepatic microRNAs identifies candidate post-transcriptional regulation networks of intermediary metabolism in rainbow trout

MicroRNAs (miRNAs) are small non-coding RNAs which act as post-transcriptional regulators by decreasing targeted mRNA translation and stability. Principally targeting small 3' UTR elements of protein-coding mRNAs through complementary base-pairing, miRNAs are promiscuous regulators of the transcriptome. While potent roles for hepatic miRNAs in the regulation of energy metabolism have emerged in rodent models, comparative roles in other vertebrates remain largely unexplored. Indeed, while several miRNAs are deeply conserved among vertebrates, the acquisition of lineage- and species-specific miRNAs, as well as the rewiring between miRNA-mRNA target relationships beg the question of regulatory and functional conservation and innovation of miRNAs and their targets involved in energy metabolism. Here we provide a meta-analysis of differentially expressed hepatic miRNAs in rainbow trout, a scientifically and economically important teleost species with a 'glucose-intolerant' phenotype. Following exposure to nutritional and social context-dependent metabolic challenges, we analyzed differential miRNA expression from small-RNA-sequencing datasets generated with a consistent bioinformatics pipeline in conjunction with an in silico target prediction of metabolic transcripts and pathways. We provide evidence for evolutionary conserved (let-7, miRNA-27 family) and rewired (miRNA-30 family, miRNA-152, miRNA-722) miRNA-metabolic target gene networks in the context of the salmonid genome. These findings represent important first steps in our understanding of the comparative regulation and function of hepatic miRNAs in rainbow trout energy metabolism. We propose that the identified miRNA families should be prioritized for future comparative functional investigation in the context of hepatic energy- and glucose metabolism in rainbow trout.

Comparative epigenetics in animal physiology: An emerging frontier

The unprecedented access to annotated genomes now facilitates the investigation of the molecular basis of epigenetic phenomena in phenotypically diverse animals. In this critical review, we describe the roles of molecular epigenetic mechanisms in regulating mitotically and meiotically stable spatiotemporal gene expression, phenomena that provide the molecular foundation for the intra-, inter-, and trans-generational emergence of physiological phenotypes. By focusing principally on emerging comparative epigenetic roles of DNA-level and transcriptome-level epigenetic mark dynamics in the emergence of phenotypes, we highlight the relationship between evolutionary conservation and innovation of specific epigenetic pathways, and their interplay as a priority for future study. This comparative approach is expected to significantly advance our understanding of epigenetic phenomena, as animals show a diverse array of strategies to epigenetically modify physiological responses. Additionally, we review recent technological advances in the field of molecular epigenetics (single-cell epigenomics and transcriptomics and editing of epigenetic marks) in order to (1) investigate environmental and endogenous factor dependent epigenetic mark dynamics in an integrative manner; (2) functionally test the contribution of specific epigenetic marks for animal phenotypes via genome and transcript-editing tools. Finally, we describe advantages and limitations of emerging animal models, which under the Krogh principle, may be particularly useful in the advancement of comparative epigenomics and its potential translational applications in animal science, ecotoxicology, ecophysiology, climate change science and wild-life conservation, as well as organismal health.

Potential regulation by miRNAs on glucose metabolism in liver of common carp (Cyprinus carpio) at different temperatures

Water temperature can affect the metabolism of fish. Common carp (Cyprinus carpio) is a representative eurythermic fish that can survive at a wide range of ambient temperatures, allowing it to live in an extensive geographical range. The goal of this work was to study the glucose metabolism of common carp at different temperatures and determine the miRNAs involved in the regulation of glucose metabolism. We determined the indicators related to glucose metabolism after long-term temperature stress and constructed nine small RNA libraries of livers under different temperature stress (5 °C, 17 °C, and 30 °C, with three biological replicates for each temperature), and subjected these samples to high-throughput sequencing. A positive relationship was observed between weight gain rate (WGR) and temperature increase after 18 days of temperature stress. However, the glucose level in the plasma maintained a gentle decrease. Unexpectedly, liver lactic acid levels were elevated in HTG (high temperature group) and LTG (low temperature group). Six down-regulated miRNAs (miR-122, miR-30b, miR-15b-5p, miR-20a-5p, miR-1, and miR-7b) were identified as involved in the regulation of glycolysis. Twelve genes were predicted as targets of these miRNAs, and these genes are in pathways related to pyruvate metabolism, glycolysis/gluconeogenesis, and the citrate cycle (TCA cycle). The results allowed prediction of a potential regulatory network of miRNAs involved in the regulation of glycolysis. The target genes of six down-regulated miRNAs were up-regulated under temperature stress, including Aldolase C, fructose-bisphosphate, b (ALDOCB), multiple inositol-polyphosphate phosphatase 1 (MINPP1), phosphoenolpyruvate carboxykinase 1 (PCK1), pyruvate dehydrogenase E1 alpha 1 (PDHA1), aldehyde dehydrogenase 9 family member A1a (ALDH9A1A), Acetyl-coenzyme A synthetase (ACSS), lactate dehydrogenase b (LDH-b), and glyoxylate reductase/hydroxypyruvate reductase (GRHPR). Other key genes of glycolysis, glucose transporter 1 (GLUT-1), pyruvate kinase PKM (PKM), and mitochondrial pyruvate carrier (MPC) were significantly up-regulated in LTG and HTG. Overall, the results suggest that miRNAs maintain their energy requirements by regulating glycolysis and play an important role in the molecular response to cold and heat stress of common carp. These data provide the foundation for further studies of the role of miRNAs in environmental adaptation in fish.