Identification of genes related to growth and amino acid metabolism from the transcriptome profile of the liver of growing laying hens
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ABSTRACT:
SUBMITTER: Wu J
PROVIDER: S-EPMC10656263 | biostudies-literature | 2023 Oct
REPOSITORIES: biostudies-literature
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Project description:BackgroundLiver is an important metabolic organ that plays a critical role in lipid synthesis, degradation, and transport; however, the molecular regulatory mechanisms of lipid metabolism remain unclear in chicken. In this study, RNA-Seq technology was used to investigate differences in expression profiles of hepatic lipid metabolism-related genes and associated pathways between juvenile and laying hens. The study aimed to broaden the understanding of liver lipid metabolism in chicken, and thereby to help improve laying performance in the poultry industry.ResultsRNA-Seq analysis was carried out on total RNA harvested from the liver of juvenile (n = 3) and laying (n = 3) hens. Compared with juvenile hens, 2567 differentially expressed genes (1082 up-regulated and 1485 down-regulated) with P ≤ 0.05 were obtained in laying hens, and 960 of these genes were significantly differentially expressed (SDE) at a false discovery rate (FDR) of ≤0.05 and fold-change ≥2 or ≤0.5. In addition, most of the 198 SDE novel genes (91 up-regulated and 107 down-regulated) were discovered highly expressed, and 332 SDE isoforms were identified. Gene ontology (GO) enrichment and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis showed that the SDE genes were most enrichment in steroid biosynthesis, PPAR signaling pathway, biosynthesis of unsaturated fatty acids, glycerophospholipid metabolism, three amino acid pathways, and pyruvate metabolism (P ≤ 0.05). The top significantly enriched GO terms among the SDE genes included lipid biosynthesis, cholesterol and sterol metabolic, and oxidation reduction, indicating that principal lipogenesis occurred in the liver of laying hens.ConclusionsThis study suggests that the majority of changes at the transcriptome level in laying hen liver were closely related to fat metabolism. Some of the SDE uncharacterized novel genes and alternative splicing isoforms that were detected might also take part in lipid metabolism, although this needs further investigation. This study provides valuable information about the expression profiles of mRNAs from chicken liver, and in-depth functional investigations of these mRNAs could provide new insights into the molecular networks of lipid metabolism in chicken liver.
| S-EPMC4600267 | biostudies-literature
Project description:Avian coccidiosis, caused by Eimeria spp, is a devastating disease in laying hens. Previous studies have suggested that amino acids may be involved in Eimeria infection of broiler chickens. However, their metabolic features in laying hens, as well as the effect of multiple Eimeria species challenges on poultry hosts have not been elucidated yet. Here, a targeted metabolomics approach was employed to identify altered amino acid metabolism and mechanisms in laying hens with multiple Eimeria species challenges. Laying hens, Hy-Line W-36 aged 25 wk, were randomly assigned to a control group and groups inoculated with varying levels of mixed Eimeria species (E. maxima, E. tenella, and E. acervulina). Serum samples from each group were collected at 6 d and 14 d of postinoculation (6 and 14 DPI) for metabolite profiling. Metabolomic analysis revealed notable metabolic variations between control and infected groups, especially at 6 DPI stage. Varying levels of Eimeria dosages did not show a significant metabolic difference, and metabolites were sensitive to low-level infection. With statistical analysis, differentially expressed compounds (3-methylhistidine, alanine, aspartate, lysine, asparagine, methionine, ornithine, and tryptophan) were selected, and their metabolic network was identified by pathway enrichment analysis. In the network, the lysine biosynthesis pathway was upregulated, while the arginine and proline metabolic pathway was downregulated under infection. Other pathways showed complex patterns of metabolic relationships. Based on the results, biological implications of metabolic changes were elucidated and discussed. Last, the results were further confirmed with our previous study (phenotype and gene expression results) using the same set of samples. Our finding provides in-depth information on altered amino acid metabolism and mechanisms in laying hens upon multiple Eimeria species infection.
| S-EPMC11407053 | biostudies-literature
Project description:In this study, RNA-Seq technology was adopted to investigate the differences in expression profiles of the hepatic lipid metabolism-related genes and the associated pathways between juvenile and laying hens. RNA-Seq analysis was carried out to estimate total RNA harvested from the liver of juvenile hens (n = 3) and laying hens (n = 3). Compared with juvenile hens, 2574 differentially expressed (DE) genes (1487 down and 1087 up) with P ≤ 0.05 were obtained, and 955 of these genes were significantly DE (SDE) at a false discovery rate (FDR) of 0.05 and fold-change ≥ 2 in laying hens. There were 198 SDE novel genes (107 down-regulated and 91 up-regulated) (FDR ≤ 0.05) that were obtained from the transcriptome, and most of them were highly expressed. Moreover, 332 SDE isoforms were identified. Gene Ontology (GO) enrichment and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis showed that SDE genes were significantly associated with steroid biosynthesis, PPAR signaling pathway, biosynthesis of unsaturated fatty acids, glycerophospholipid metabolism, three amino acid pathways, and pyruvate metabolism (P ≤ 0.05). The top significantly enriched GO terms included lipid biosynthesis, cholesterol and sterol metabolic, and oxidation reduction suggesting the principal lipogenesis in the liver of laying hens. This study suggests that the major changes at the level of transcriptome in laying hen liver are closely related to fat metabolism. Some highly differentially expressed uncharacterized novel genes and alternative splicing isoforms detected might also take part in lipid metabolism, though it needs investigation. Therefore, this study provides valuable information of mRNA of chicken liver, and deeper functional investigations on the mRNAs could help explore or provide new insights into molecular networks of lipid metabolism in chicken liver.
2016-01-08 | GSE70010 | GEO
Project description:In this study, RNA-Seq technology was adopted to investigate the differences in expression profiles of the hepatic lipid metabolism-related genes and the associated pathways between juvenile and laying hens. RNA-Seq analysis was carried out to estimate total RNA harvested from the liver of juvenile hens (n = 3) and laying hens (n = 3). Compared with juvenile hens, 2574 differentially expressed (DE) genes (1487 down and 1087 up) with P ⤠0.05 were obtained, and 955 of these genes were significantly DE (SDE) at a false discovery rate (FDR) of 0.05 and fold-change ⥠2 in laying hens. There were 198 SDE novel genes (107 down-regulated and 91 up-regulated) (FDR ⤠0.05) that were obtained from the transcriptome, and most of them were highly expressed. Moreover, 332 SDE isoforms were identified. Gene Ontology (GO) enrichment and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis showed that SDE genes were significantly associated with steroid biosynthesis, PPAR signaling pathway, biosynthesis of unsaturated fatty acids, glycerophospholipid metabolism, three amino acid pathways, and pyruvate metabolism (P ⤠0.05). The top significantly enriched GO terms included lipid biosynthesis, cholesterol and sterol metabolic, and oxidation reduction suggesting the principal lipogenesis in the liver of laying hens. This study suggests that the major changes at the level of transcriptome in laying hen liver are closely related to fat metabolism. Some highly differentially expressed uncharacterized novel genes and alternative splicing isoforms detected might also take part in lipid metabolism, though it needs investigation. Therefore, this study provides valuable information of mRNA of chicken liver, and deeper functional investigations on the mRNAs could help explore or provide new insights into molecular networks of lipid metabolism in chicken liver. The liver expression profile of juvenile hens and laying hens were generated by RNA-seq.
2016-01-08 | E-GEOD-70010 | biostudies-arrayexpress
Project description:Exposure to high ambient temperature has detrimental effects on poultry welfare and production. Although changes in gene expression due to heat exposure have been well described for broiler chickens, knowledge of the effects of heat on laying hens is still relatively limited. In this study, we profiled the transcriptome for pectoralis major muscle (n = 24) and liver (n = 24), during a 4-week cyclic heating experiment performed on layers in the early phase of egg production. Both heat-control and time-based contrasts were analyzed to determine differentially expressed genes (DEGs). Heat exposure induced different changes in gene expression for the two tissues, and we also observed changes in gene expression over time in the control animals suggesting that metabolic changes occurred during the transition from onset of lay to peak egg production. A total of 73 DEGs in liver were shared between the 3 h heat-control contrast, and the 4-week versus 3 h time contrast in the control group, suggesting a core set of genes that is responsible for maintenance of metabolic homeostasis regardless of the physiologic stressor (heat or commencing egg production). The identified DEGs improve our understanding of the layer's response to stressors and may serve as targets for genetic selection in the future to improve resilience.
| S-EPMC7916550 | biostudies-literature
Project description:Probiotic Clostridium butyricum could affect lipid metabolism in broilers. However, it is not clear whether C. butyricum could improve lipid metabolism through shaping gut microbiota and bile acid (BA) profile of laying hens. We aimed to evaluate the contributions of gut microbiota and BA profile to the potential effect of C. butyricum on lipid metabolism of aged laying hens. A total of 192 60-week-old Hy-Line Brown laying hens were divided into two groups (eight replicates per group). Birds were fed a basal diet supplemented with 0 or 2.7 g/kg C. butyricum (1.0 × 109 CFU/g). Samples were collected at the end of week 8 of the experiment. The results showed elevated (P < 0.05) concentrations of glucagon-like peptide 1, insulin and thyroid hormones in serum responded to C. butyricum addition, which also decreased (P < 0.05) hepatic free fatty acids contents, as well as increased (P < 0.05) the expression of hepatic acyl-CoA oxidase, farnesoid X receptor (FXR) and PPARα. C. butyricum addition increased (P < 0.05) Bacteroidetes abundance but tended to decrease (P < 0.10) Firmicutes abundance in the ileum. Besides, C. butyricum addition resulted in higher (P < 0.05) abundances of Clostridia (Clostridiales) and Prevotellaceae, concurrent with an increasing trend (P < 0.10) of Bifidobacteriaceae abundance and decreased the abundances of several harmful bacteria such as Klebsiella (P < 0.05). Regarding ileal BA profile, there was a reduced (P < 0.05) content of tauro-α-muricholic acid, increased (P < 0.05) contents of tauroursodeoxycholic acid and lithocholic acid, along with increasing trends (P < 0.10) of glycochenodeoxycholic acid and hyodeoxycholic acid contents due to C. butyricum addition, which also increased (P < 0.05) ileal FXR expression. Collectively, supplemental C. butyricum accelerated hepatic fatty acid oxidation, and shaped gut microbiota and BA profile, thus reducing fat deposition in the liver of aged laying hens.
| S-EPMC7176355 | biostudies-literature
Project description:This study aimed to investigate the age-related changes of hepatic metabolism and antioxidant capacity of laying hens at 3 different ages. A total of 192 Hy-line Brown laying hens were assigned into 3 groups: 1) 195-day-old (D195 group); 2) 340-day-old (D340 group); 3) 525-day-old (D525 group). Each group replicated 8 times with 8 hens at the same age. Higher activity of aspartate aminotransferase and lower contents of total protein and globulin were observed in the serum of 525-day-old hens in comparison with their 195-day-old counterparts (P < 0.05). The 525-day-old hens accumulated higher contents of total cholesterol and triglyceride in the liver than 195-day-old birds. Additionally, compared with hens from D195 or D340 group, 525-day-old birds exhibited a lower circulating estradiol level (P < 0.05). For antioxidant capacity, birds in the D525 group showed a higher malondialdehyde concentration in both serum and liver as compared with D195 or D340 group (P < 0.05). The 525-day-old hens also exhibited lower glutathione peroxidase activities in both serum and liver when compared with 195-day-old birds (P < 0.05). Simultaneously, there was a decline of hepatic superoxide dismutase activity in the D525 group in comparison with D195 group (P < 0.05). Compared with 195-day-old counterparts, 340-day-old birds upregulated the mRNA abundance of nuclear factor erythroid-2 related factor 2 and glutathione peroxidase 1 in the liver (P < 0.05). In contrast, hens from D525 group showed the downregulation of hepatic nuclear factor erythroid-2 related factor 2, NAD(P)H quinone dehydrogenase 1, and superoxide dismutase 1 when compared with D340 group (P < 0.05). These results indicated that increasing age can adversely affect liver metabolism and function of laying hens.
| S-EPMC8554276 | biostudies-literature
Project description:Non-alcoholic fatty liver disease (NAFLD) is a chronic and metabolic liver disease and commonly occurs in humans with obesity and type 2 diabetes mellitus (T2DM); such a condition also exists in animals such as rodents and laying hens. Since the pathogenesis of fatty liver hemorrhagic syndrome (FLHS) of laying hens is similar to human NAFLD, hen's FLHS is commonly selected as a study model of NAFLD. Altered circulating amino acids, particularly elevated branched-chain amino acids (BCAAs) and aromatic amino acids (AAAs), are consistently reported in patients with NAFLD and T2DM. How long-term dietary individual BCAA, such as valine, impacts amino acid and fatty acid metabolism remains unknown. In this study, we demonstrated that when laying hens are fed with dietary valine at different levels (59, 0.64, 0.69, 0.74, and 0.79%) in a feeding trial that lasted for 8 weeks, long-term exposure to excessive valine diets at 0.74 and 0.79% levels could induce amino acid imbalance, impair amino acid metabolism, increase fatty acid synthesis, and inhibit fatty acid utilization. Long-term intake of excessive dietary valine could result in impaired amino acid metabolism via inhibiting C/EBP-β/asparagine synthetase (Asns). This process is mediated by downregulating the general control nonderepressible-eukaryotic initiation factor 2α- activating transcription factor (GCN2-eIF2α-ATF4) pathway and elevating corresponding circulating BCAAs and AAAs levels, which could ultimately result in amino acid imbalance. High levels of dietary valine stimulated lipid deposition by suppressing the GCN2-eIF2α-ATF4-fibroblast growth factor-19 (FGF19)-target of rapamycin complex 1 (TORC1) signaling pathway to promote fatty acid synthesis, repress fatty acid utilization, and eventually accelerate the development of NAFLD. The Spearman correlation analysis revealed that circulating amino acid imbalance is significantly associated with fatty acid metabolism disorder and enhanced oxidative stress. The inhibition of the GCN2-TORC1 pathway induced autophagy suppression to trigger liver oxidative stress and inflammatory response. In conclusion, our results revealed the adverse metabolic response to excessive dietary valine mediated by amino acid and fatty acid metabolism disorders. This study also suggested reducing dietary valine as a novel approach to preventing and treating NAFLD in humans and FLHS in laying hens.
| S-EPMC9040670 | biostudies-literature
Project description:As the extension of the egg-laying cycle, heightened energy and lipid metabolism cause excessive lipid accumulation, resulting in rapid decline in laying performance during the late laying period. Bile acids (BAs), synthesized from cholesterol in the liver, are potent metabolic and immune signaling molecules involved in lipid metabolism and the regulation of energy homeostasis. However, under different dietary protein levels, the role of BAs on hepatic lipid metabolism of laying hens at the late phase remains unclear. This experiment aimed to evaluate the effects of porcine BAs supplementation on performance, lipid metabolism, antioxidant status and amino acid metabolism in late-phase laying hens fed diets with different protein level. A total of 192 Hy-Line Brown laying hens (62 weeks of age) were randomly assigned to one of four treatment groups, in a 2 × 2 factorial design, with 8 replicates per treatment. The hens were fed diets with either normal protein (16.42 %) or low-protein (15.35 %) levels, with or without BAs supplementation (120 mg/kg for the first 56 days, followed by 200 mg/kg for the next 42 days). The results demonstrated that dietary BAs supplementation significantly enhanced egg production and feed intake (P < 0.05) although it has no notable effect on egg quality. Bile acids supplementation effectively reduced liver total cholesterol (TC), triglyceride (TG), as well as malondialdehyde (MDA) levels, while also ameliorating lipid deposition through the regulation of expression of lipid metabolism-related genes in late laying hens (P < 0.05). Additionally, the low-protein diets downregulated amino acid catabolism, thereby reducing serum uric acid content and enhancing protein utilization. Further analysis revealed that BAs also positively influenced trypsin activity and increased the expression of amino acid transporters, thereby improving amino acid availability (P < 0.05). In conclusion, this study demonstrated that dietary BAs supplementation could enhance the laying performance in late laying hens, primarily by improving hepatic lipid metabolism, antioxidant capacity, and amino acid availability.
| S-EPMC11782899 | biostudies-literature
Project description:Moult is a normal physiological phenomenon in poultry. Induced molting (IM) is the most widely used and economical molting technique. By inducing moult, the laying hens can grow new feathers during the next laying cycle and improve laying performance. However, the lack of energy supply has a huge impact on both the liver and intestines and acts on the intestines and liver through the "gut-liver axis". More importantly, lipid metabolism in the liver is closely related to the laying performance of laying hens. Therefore, in this study, cecal metabolites and liver transcriptome data during IM of laying hens at the late stage of laying (stop feeding method) were analyzed together to reveal the regulatory mechanism of "gut-liver axis" affecting the laying performance of laying hens from the perspective of lipid metabolism. Transcriptome analysis revealed that 4,796 genes were obtained, among which 2,784 genes had significant differences (p < 0.05). Forty-nine genes were associated with lipid metabolism, and five core genes (AGPAT2, SGPL1, SPTLC1, PISD, and CYP51A1) were identified by WGCNA. Most of these differential genes are enriched in steroid biosynthesis, cholesterol metabolism, drug metabolism-cytochrome P450, synthesis and degradation of ketone bodies, PPAR signaling pathway, and bile secretion. A total of 96 differential metabolites were obtained by correlating them with metabolome data. Induced moult affects laying performance by regulating genes related to lipid metabolism, and the cecal metabolites associated with these genes are likely to regulate the expression of these genes through the "enterohepatic circulation". This experiment enriched the theoretical basis of induced moult and provided the basis for prolonging the feeding cycle of laying hens.
| S-EPMC9169092 | biostudies-literature