Identification and characterization of lipid metabolism-related microRNAs in the liver of genetically improved farmed tilapia (GIFT, Oreochromis niloticus) by deep sequencing

Effects of Fat and Carnitine on the Expression of Carnitine Acetyltransferase and Enoyl-CoA Hydratase Short-Chain 1 in the Liver of Juvenile GIFT (Oreochromis niloticus)

Carnitine acetyltransferase (CAT) and Enoyl-CoA hydratase short-chain 1 (ECHS1) are considered key enzymes that regulate the β-oxidation of fatty acids. However, very few studies have investigated their full length and expression in genetically improved farmed tilapia (GIFT, Oreochromis niloticus), an important aquaculture species in China. Here, we cloned CAT and ECHS1 full-length cDNA via the rapid amplification of cDNA ends, and the expressions of CAT and ECHS1 in the liver of juvenile GIFT were detected in different fat and carnitine diets, as were the changes in the lipometabolic enzymes and serum biochemical indexes of juvenile GIFT in diets with different fat and carnitine levels. CAT cDNA possesses an open reading frame (ORF) of 2167 bp and encodes 461 amino acids, and the ECHS1 cDNA sequence is 1354 bp in full length, the ORF of which encodes a peptide of 391 amino acids. We found that juvenile GIFT had higher lipometabolic enzyme activity and lower blood CHOL, TG, HDL-C, and LDL-C contents when the dietary fat level was 2% or 6% and when the carnitine level was 500 mg/kg. We also found that the expression of ECHS1 and CAT genes in the liver of juvenile GIFT can be promoted by a 500 mg/kg carnitine level and 6% fat level feeding. These results suggested that CAT and ECHS1 may participate in regulating lipid metabolism, and when 2% or 6% fat and 500 mg/kg carnitine are added to the feed, it is the most beneficial to the liver and lipid metabolism of juvenile GIFT. Our results may provide a theoretical basis for GIFT feeding and treating fatty liver disease.

Isoliquiritigenin-mediated miR-23a-3p inhibition activates PGC-1α to alleviate alcoholic liver injury

BACKGROUND

Alcoholic liver disease (ALD), one of the most prevalent forms of liver disease, has received wide attention worldwide. However, limited efficient and appropriate therapeutic agents were responded to ALD. Isoliquiritigenin (ISL), a flavonoid isolated from liquorice, possesses multiple pharmacological activities.

PURPOSE

The current study investigated the hepatoprotective effect of ISL against ALD and further elucidate the involvement of miR-23a-3p/peroxisome proliferative activated receptor-γ coactivator 1 alpha (PGC-1α) in vivo and in vitro experiments.

STUDY DESIGN AND METHODS

In the study, H&E and Oil Red O staining were employed to detect liver histopathological changes and the accumulation of lipid droplets. Quantitative real-time PCR, bioinformatics, luciferase assay, immunofluorescence staining, reactive oxygen species (ROS), Western blot, and siRNA were used to further explore the mechanism of ISL protection.

RESULTS

ISL significantly reduced the liver-to-body weight ratios and biochemical index. The staining results showed that ISL remarkedly ameliorated the histopathological changes in the liver. Furthermore, ISL promoted fatty acid metabolism via induction in the expression of PGC-1α-target genes PPARα, CPT1α, and ACADs, and inhibited the ROS, TNF-α, IL-1β, and IL-6 expression. Bioinformatics and Luciferase assay analysis confirmed that miR-23a-3p might bind to PGC-1α mRNA in ALD. Significantly, the expression of miR-23a-3p was increased in the ALD, which was significantly decreased by ISL. In addition, the miR-23a-3p inhibitor also promoted lipid metabolism in ALD via PGC-1α activation.

CONCLUSIONS

We first demonstrated that ISL could alleviate ALD, and further verified that ISL exerted protective effects through modulating miR-23a-3p/PGC-1α-mediated lipid metabolism in vivo and in vitro.

Metabolism and antioxidation regulation of total flavanones from Sedum sarmentosum Bunge against high-fat diet-induced fatty liver disease in Nile tilapia (Oreochromis niloticus)

Diet-induced fatty liver is a considerable threaten to fish aquaculture due to the popularity of the high-fat diet (HFD) feeding. Our study aims to investigate the effects of flavanones from Sedum sarmentosum Bunge (FSSB) on the liver function to identify a potential treatment for HFD-induced fatty liver disease. Physiological and pathological indicators were tested in the liver of Nile tilapia (Oreochromis niloticus) and results showed parameters including lipid metabolites, redox parameters, and inflammatory factors could be adequately restored to normal level by addition of 150 mg/kg FSSB to HFD. Proteomics analysis was performed in liver tissues from tilapia with normal diet (ND), HFD, and HFD+FSSB. Totally, 51 upregulated proteins and 77 downregulated proteins were identified in HFD groups and 67 proteins of them were restored after treated with FSSB. Bioinformatics analysis showed that differentially expressed proteins (DEPs) in HFD+FSSB150 group compared with HFD group are mainly enriched in acety-CoA metabolic process, adenosine-triphosphate (ATP) biosynthetic process, lipid metabolic process, and phospholipid metabolic process. The dysregulated proteins were involved in peroxidosome proliferators-activated receptor (PPAR) signaling pathway, fat digestion and absorption, and immune system. The quantitative real-time PCR (qRT-PCR) assay further revealed that the expression of GST, PPARα, PPARγ, and multiple-inflammatory cytokines could be also reversed in HFD group under the treatment of 150 mg/kg FSSB. Our findings demonstrated FSSB is efficient for the treatment of fatty liver disease through regulation of lipid metabolism and antioxidation in Nile tilapia, providing a new treatment of non-alcoholic fatty liver disease (NAFLD) in fish aquaculture.

Expression profile of miRNAs involved in the hepatoprotective effects of curcumin against oxidative stress in Nile tilapia

Curcumin is a polyphenol with antioxidant activity that has been used to protect the health of fish livers. Our previous studies about comparative transcriptome have shown that curcumin can enhance the Nrf2-Keap1 signaling pathway and induce downstream anti-stress genes to maintain cell viability. However, the possible role of miRNAs in the protective mechanism of curcumin is not understood. In this study, the tilapia hepatocyte H₂O₂ stress model was used, and the miRNA expression profile for four groups (control group, curcumin group, H₂O₂ group, and protection group) were established by high-throughput sequencing. In our results, 278-333 types of Oreochromis niloticus miRNAs, 309-543 types of conserved miRNAs, and 535-746 types of novel miRNAs were identified in different samples. Differentially expressed miRNAs were identified by comparing miRNA expression profiles among the four groups. The expression levels were confirmed by q-PCR. The target genes of these differentially expressed miRNAs were predicted, and their functional annotations were enriched by GO and KEGG analysis, which revealed that many target genes were involved in "response to stimulus" and "antioxidant activity" in each pair of groups. Several miRNAs related to oxidative stress showed differential expression. For example, in the H₂O₂ group, the expression of miR-122 was decreased, and the expression of miR-21 and miR-489 increased significantly. In the curcumin group, the expression of miR-153b was decreased, and the expression of miR-200a and miR-29 was increased significantly. miR-153b, miR-200a, and miR-29 may be involved in the regulation of the Nrf2-Keap1 signaling pathway by curcumin. This work might provide insights into the molecular mechanisms of miRNA regulation of curcumin on the prevention and alleviation of liver diseases in fish.

Low expression of miR-19a-5p is associated with high mRNA expression of diacylglycerol O-acyltransferase 2 (DGAT2) in hybrid tilapia

DGAT2 (acyl CoA:diacylglycerol acyltransferase 2) is a key and rate-limiting enzyme that catalyzes the final step of triglyceride (TG) synthesis. In this study, hybrid tilapia were generated from Nile tilapia (♀) and blue tilapia (♂) crossing. The TG content levels in the liver of these tilapia were measured. The results showed that the TG content was higher in the hybrid tilapia. In addition, protein and mRNA expression levels in the tilapia livers were determined. Higher hepatic mRNA and protein expression of DGAT2 in the hybrid fish was found. A luciferase reporter assay with HEK293T cells revealed that miRNA-19a-5p targeted the 3'UTR of DGAT2, suggesting a direct regulatory mechanism. Using qRT-PCR, we found that DGAT2 mRNA levels had a negative correlation with miRNA-19a-5p expression in Nile tilapia and hybrid. Taken together, these findings provide evidence that miRNA-19a-5p is involved in TG synthesis in the regulation of lipid metabolism in tilapia.

Modulation of hepatic miRNA expression in Atlantic salmon (Salmo salar) by family background and dietary fatty acid composition

This study finds significant differences in hepatic fatty acid composition between four groups of Atlantic salmon (Salmo salar) consisting of offspring from families selected for high and low capacities to express the delta 6 desaturase isomer b and fed diets with 10% or 75% fish oil. The results demonstrated that hepatic lipid metabolism was affected by experimental conditions (diet/family). The fatty acid composition in the four groups mirrored the differences in dietary composition, but it was also associated with the family groups. Small RNA sequencing followed by RT-qPCR identified 12 differentially expressed microRNAs (DE miRNAs), with expression associated with family groups (miR-146 family members, miR-200b, miR-214, miR-221, miR-125, miR-135, miR-137, miR_nov_1), diets (miR-203, miR-462) or both conditions. All the conserved DE miRNAs have been reported as associated with lipid metabolism in other vertebrates. In silico predictions revealed 37 lipid metabolism pathway genes, including desaturases, transcription factors and key enzymes in the synthesis pathways as putative targets (e.g., srebp-1 and 2, Δ6fad_b and c, hmdh, elovl4 and 5b, cdc42). RT-qPCR analysis of selected target genes showed expression changes that were associated with diet and with family groups (d5fad, d6fad_a, srebp-1). There was a reciprocal difference in the abundance of ssa-miR-203a-3p and srebp-1 in one group comparison, whereas other predicted targets did not reveal any evidence of being negatively regulated by degradation. More experimental studies are needed to validate and fully understand the predicted interactions and how the DE miRNAs may participate in the regulation of hepatic lipid metabolism.

Responses of functional miRNA-mRNA regulatory modules to a high-fat diet in the liver of hybrid yellow catfish (Pelteobagrus fulvidraco × P. vachelli)

Fatty liver disease is common in cultured yellow catfish as a result of high fat contents in feeds. However, little is known about the mechanism by which the excessive deposition of liver fat causes fatty liver disease. Hybrid yellow catfish (Pelteobagrus fulvidraco♀ × P. vachelli♂) were fed a high-fat diet (HFD) or a normal-fat diet (NFD) for 60 days. Compared with the NFD group, the HFD group showed lower growth performance, higher hepatosomatic and viscerosomatic indexes, increased hepatic triglyceride and cholesterol contents, and more and larger lipid droplets in liver tissue. Whole transcriptome mRNA libraries and microRNA libraries from fish in the NFD and HFD groups were constructed by high-throughput sequencing. Twelve miRNAs were differentially expressed (DE) between the HFD and NFD groups. Seven negatively correlated DE miRNA-DE mRNA pairs were selected, and the expression patterns of both were confirmed using qRT-PCR. Hybrid yellow catfish showed mediated oxidative degradation of liver glucose and fatty acid peroxidation, regulation of antioxidant enzyme activity, and various immune and inflammatory responses to fat deposition and stress. These findings have important biological significance for protecting the liver against stress, as well as economic significance for establishing healthy aquaculture conditions.

miR-34a Regulates the Activity of HIF-1a and P53 Signaling Pathways by Promoting GLUT1 in Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) Under Hypoxia Stress

In fish under hypoxia stress, homeostasis can become imbalanced, leading to tissue and organ damage and decreased survival. Therefore, it is useful to explore the molecular and physiological regulation mechanisms that function in fish under hypoxia stress. The microRNA miR-34a is involved in fat and glycogen metabolism, and in apoptosis. In this study, we first verified that GLUT1, the gene encoding glucose transporter 1, is a potential target gene of miR-34a in genetically improved farmed tilapia (GIFT, Oreochromis niloticus) by dual luciferase reporter assays. Then, we clarified the regulatory relationship between miR-34a and GLUT1 by qRT-PCR analyses. We analyzed the regulatory effects of knockdown or promotion of GLUT1 expression in vitro and in vivo in GIFT under hypoxia stress. The results confirm that GLUT1 is a target gene of miR-34a in GIFT. Down-regulation of miR-34a significantly promoted GLUT1 expression. Knockdown of GLUT1 reduced the glycogen content in GIFT liver cells, inhibited HIF-1a gene expression, up-regulated the expression of genes involved in P53 signaling pathways (P53 and CASPASE-3 genes), and accelerated hepatocyte apoptosis under hypoxia stress. Compared with the control group, the group injected in the tail vein with miR-34a antagomir showed up-regulated expression of GLUT1 in the liver, increased liver glycogen content at 96 h of hypoxia stress, down-regulated expression of P53 and CASPASE-3, and decreased serum aspartate aminotransferase and alanine aminotransferase enzyme activities. Our results provide information about the molecular regulation mechanism of miRNAs and their target genes in fish during the response to hypoxia stress.

MicroRNA-23a suppresses the apoptosis of inflammatory macrophages and foam cells in atherogenesis by targeting HSP90

In previous study, we have found that microRNA-23a is down regulated in atherosclerotic tissues. Here we demonstrate that miR-23a directly binds to 3'UTR of HSP90 mRNA to suppress the expression of HSP90. To investigate the potential roles of miR-23a in macrophage, THP-1 macrophages were transfected with miR-23a mimics or inhibitors. Our results showed inflammatory factors IL-6 and MCP-1 concentrations in cell culture medium of macrophage and foam cell transfected with miR-23a mimics were decreased. Furthermore, we find that apoptosis of macrophage and foam cells transfected with miR-23a mimics were inhibited. Over expression of miR-23a in foam cells could reduced lipid intake and accumulation in foam cells. Meanwhile, we found that in inflammatory macrophages and foam cells transfected with miR-23a mimcs, HSP90 and NF-κB proteins are significantly decreased. Our results have suggested a promising and potential therapeutic target for atherosclerosis.

New Insights on Intermediary Metabolism for a Better Understanding of Nutrition in Teleosts

The rapid development of aquaculture production throughout the world over the past few decades has led to the emergence of new scientific challenges to improve fish nutrition. The diet formulations used for farmed fish have been largely modified in the past few years. However, bottlenecks still exist in being able to suppress totally marine resources (fish meal and fish oil) in diets without negatively affecting growth performance and flesh quality. A better understanding of fish metabolism and its regulation by nutrients is thus mandatory. In this review, we discuss four fields of research that are highly important for improving fish nutrition in the future: ( a) fish genome complexity and subsequent consequences for metabolism, ( b) microRNAs (miRNAs) as new actors in regulation of fish metabolism, ( c) the role of autophagy in regulation of fish metabolism, and ( d) the nutritional programming of metabolism linked to the early life of fish.

Changes in Physiological Parameters, Lipid Metabolism, and Expression of MicroRNAs in Genetically Improved Farmed Tilapia (Oreochromis niloticus) With Fatty Liver Induced by a High-Fat Diet

Tilapia is susceptible to hepatic steatosis when grown in intensive farming systems. The aim of this study was to explore the mechanism of fatty liver induced by a high-fat diet (HFD) in genetically improved farmed tilapia (GIFT, Oreochromis niloticus). Juvenile GIFT were fed with HFD or a normal-fat diet (NFD) for 60 days. Substantial fat deposition in the liver of HFD-fed GIFT on days 20, 40, and 60 was observed using hematoxylin – eosin staining and oil red O staining. The increased fat deposition was consistent with increased triglyceride (TG) and total cholesterol (TC) levels in the liver of HFD-fed GIFT. There were significant differences (P < 0.05) in serum biochemical indexes (TG, TC, low density lipoprotein-cholesterol, and insulin contents, and alanine aminotransferase activity) between GIFT fed a HFD and GIFT fed a NFD on days 20, 40, and 60. Furthermore, 60 days of a HFD significantly changed (P < 0.05) the hepatic fatty acid composition, and led to increased polyunsaturated fatty acid levels and decreased saturated fatty acid and monounsaturated fatty acid levels. Hepatic antioxidant enzyme activities increased by day 20 and then declined, which led to an increase in malondialdehyde contents in the liver of HFD-fed GIFT. Molecular analyses revealed that the microRNAs miR-122, miR-29a, and miR-145-5p were upregulated, whereas miR-34a was downregulated in HFD-fed GIFT. SCD, ELOVL6, and SRD5A2 encode three important enzymes in lipid metabolism, and were identified as potential targets of miRNAs. The transcript levels of hepatic SCD and ELOVL6 were decreased and that of hepatic SRD5A2 was increased in GIFT fed a HFD. Overall, the results of this study revealed a potential link between miRNAs and fatty liver induced by HFD, and suggest that a HFD could lead to excess fat deposition in the GIFT liver, which may disrupt hepatic lipid metabolism and reduce the antioxidant defense capacity.

High Fat Diet-Induced miR-122 Regulates Lipid Metabolism and Fat Deposition in Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) Liver

The liver is an important organ for the regulation of lipid metabolism. In genetically improved farmed tilapia (GIFT, Oreochromis niloticus), fat deposition in the liver occurs when they are fed high-lipid diets over a long term. This can affect their growth, meat quality, and disease resistance. MicroRNAs (miRNAs) are known to be crucial regulatory factors involved in lipid metabolism; however, the mechanism by which they regulate lipid deposition in GIFT remains unclear. Comparative miRNA expression profiling between GIFT fed a normal diet and those fed a high-lipid diet showed that miR-122 is closely related to lipid deposition. Using miR-122 as a candidate, we searched for a binding site for miR-122 in the 3'-untranslated region (UTR) of the stearoyl-CoA desaturase gene (SCD) using bioinformatics tools, and then confirmed its functionality using the luciferase reporter gene system. Then, the regulatory relationship between this miRNA and its target gene SCD was analyzed using real-time polymerase chain reaction (qRT-PCR) and western blotting analyses. Last, we investigated the effect of the loss of miR-122 expression on lipid metabolism in GIFT. The results showed that a sequence in the 3'-UTR region of SCD of GIFT was complementary to the miR-122 seed region, and there was a negative relationship between the expression of miRNA and SCD expression. Inhibition of miR-122 up-regulated SCD, increased the expression of fat synthesis-related genes, increased hepatic triglyceride and cholesterol contents, and promoted weight gain in fish. Our results showed that miR-122 targets SCD to mediate hepatic fat metabolism. These results provide new insights for the prevention and treatment of fatty liver disease in GIFT.

MiR-27a-5p Increases Steer Fat Deposition Partly by Targeting Calcium-sensing Receptor (CASR)

Castration increases fat deposition, improving beef quality in cattle. Here, the steer group exhibited a significantly higher intramuscular fat (IMF) content than the bull group. To determine the potential roles of microRNAs (miRNAs) in castration-induced fat deposition, differential expression patterns of miRNA in liver tissue were investigated in bulls and steers. A total of 7,827,294 clean reads were obtained from the bull liver library, and 8,312,483 were obtained from the steer liver library; 452 conserved bovine miRNAs and 20 novel miRNAs were identified. The results showed that the expression profiles of miRNA in liver tissue were changed by castration, and 12 miRNAs that were differentially expressed between bulls and steers were identified. Their target genes were majorly involved in the metabolic, PI3K-Akt, and MAPK signaling pathways. Furthermore, six differentially expressed miRNAs were validated by quantitative real-time PCR, and luciferase reporter assays verified that calcium-sensing receptor (CASR) was the direct target of miR-27a-5p. Meantime, we found that the expression level of CASR was significantly higher in steers than in bulls, and revealed that CASR gene silencing in bovine hepatocytes significantly inhibited triacylglycerol (TAG) accumulation and reduced secretion of very low density lipoprotein (VLDL). These results obtained in the liver indicate that miR-27a-5p may increase fat deposition partly by targeting CASR in steers.