Identification of genes related to dexamethasone-induced immunosuppression in chicken thymus using transcriptome analysis

Impacts of longitudinal water curtain cooling system on transcriptome-related immunity in ducks

BACKGROUND

The closed poultry houses integrated with a longitudinal water curtain cooling system (LWCCS) are widely used in modern poultry production. This study showed the variations in environmental conditions in closed houses integrated with a longitudinal water curtain cooling system. We evaluated the influence of different environmental conditions on duck growth performance and the transcriptome changes of immune organs, including the bursa of Fabricius and the spleen.

RESULT

This study investigated the slaughter indicators and immune organ transcriptomes of 52-day-old Cherry Valley ducks by analyzing the LWCC at different locations (water curtain end, middle position, and fan cooling end). The results showed that the cooling effect of the LWCCS was more evident from 10:00 a.m. -14:00. And from the water curtain end to the fan cooling end, the hourly average temperature differently decreased by 0.310℃, 0.450℃, 0.480℃, 0.520℃, and 0.410℃, respectively (P < 0.05). The daily and hourly average relative humidity decreased from the water curtain end to the fan cooling end, dropping by 7.500% and 8.200%, respectively (P < 0.01). We also observed differences in production performance, such as dressing weight, half-eviscerated weight, skin fat rate, and percentage of abdominal fat (P < 0.01), which may have been caused by environmental conditions. RNA-sequencing (RNA-seq) revealed 211 and 279 differentially expressed genes (DEGs) in the ducks' bursa of Fabricius and spleen compared between the water curtain end and fan cooling end, respectively. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the two organs showed the DEGs were mainly enriched in cytokine-cytokine receptor interaction, integral component of membrane, Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) signaling pathway, etc. Our results implied that full-closed poultry houses integrated with LWCCS could potentially alter micro-environments (water curtain vs. fan cooling), resulting in ducks experiencing various stressful situations that eventually affect their immunity and production performance.

CONCLUSION

In this study, our results indicated that uneven distributions of longitudinal environmental factors caused by LWCCS would affect the dressed weight, breast muscle weight, skin fat rate, and other product performance. Moreover, the expression of immune-related genes in the spleen and bursa of ducks could be affected by the LWCCS. This provides a new reference to optimize the use of LWCCS in conjunction with close duck houses in practical production.

Modulation of inflammatory and oxidative stress biomarkers due to dexamethasone exposure in chicken splenocytes

Dexamethasone (DEXA) is a potent corticosteroid, commonly used for treating inflammatory, hypersensitive and allergic conditions. It is administered to birds with tumours. Many studies were conducted on its immunosuppressive effects; however none of the similar study is available employing chicken splenocytes culture system. The present study was conducted to assess DEXA induced alterations in inflammatory and oxidative stress biomarkers in chicken splenocytes due to its in vitro exposure. The maximum non-cytotoxic dose (MNCD) was evaluated and was further used for conducting lymphocytes proliferation assay (LPA), antioxidant assays (lipid peroxidation, GSH, superoxide dismutase and nitric oxide assays) and assessment of mRNA levels of various genes (IL-1β, IL-6, IL-10, LITAF, iNOS, NF-κB1, Nrf-2, Caspase-3 and -9) through qPCR. The MNCD was determined to be 30 ng/ml in chicken splenocytes culture system. DEXA caused reduction in B and T lymphocytes proliferation indicating its immunosuppressive effects, however improved the antioxidant status of the exposed splenocytes. The expression levels of IL-1β, IL-6, iNOS, LITAF and NF-κB1 were significantly reduced while IL-10 was enhanced, which signify potent anti-inflammatory potential of DEXA. NF-κB is a major transcription factor that regulates genes responsible for both, innate and adaptive immune responses and elicits inflammation. The nuclear factor erythroid 2-related factor 2 (Nrf-2) level was found to be up-regulated. Nrf-2 plays important role in combating the oxidant stress and its increased expression could be the reason of improved antioxidant status of DEXA exposed cells. Present findings indicated that DEXA exhibited modulation in anti-inflammatory, immunomodulatory and antioxidant mediators in chicken splenocytes.

Integrative analysis of transcriptome and metabolome reveals probiotic effects on cecal metabolism in broilers

BACKGROUND

Probiotics play an important role in the host and have attracted widespread attention as an alternative to antibiotics. Arbor Acres broilers were used in the present experiment and fed different doses of compound probiotics at 1, 5, and 10 g kg^-1 . The effects of compound probiotics on broiler growth performance and cecal transcriptome and metabolome were investigated.

RESULTS

We discovered 425 differentially expressed genes (DEGs; upregulated: 256; downregulated: 169) in the cecal transcriptome study. These DEGs were assigned to fat metabolic pathways, such as the peroxisome proliferator-activated receptor (PPAR) signaling pathway, according to KEGG analysis. Probiotics downregulated LPL and upregulated PPARα expression in the cecum. In metabolome analysis of the cecum of cecum, we screened 86 differential metabolites and performed KEGG enrichment analysis of these metabolites. The KEGG analysis showed that these differentially expressed metabolites were annotated to nucleotide metabolism-related pathways, such as purine metabolism. In the cecum, probiotics upregulated the content of guanine, AMP, 3'-AMP, adenylosuccinate, deoxyguanosine, and ADP-ribose, whereas they downregulated the content of 5-hydroxyisourate. Comprehensive transcriptome and metabolome analysis revealed that glycolysis, gluconeogenesis, and glycerophospholipid metabolism pathways were jointly enriched in cecum of broilers fed a probiotic-containing diet.

CONCLUSION

This study provides valuable information for studying the regulation and gene metabolism network of probiotics on cecal metabolism in broilers. © 2022 Society of Chemical Industry.

Stress-induced immunosuppression affecting immune response to Newcastle disease virus vaccine through "miR-155-CTLA-4" pathway in chickens

MiR-155 and CTLA-4 are important factors involved in the regulation of immune function. However, there is no report about their involvement in function regulation of stress-induced immunosuppression affecting immune response. In this study, the chicken model of stress-induced immunosuppression affecting immune response (simulation with dexamethasone and immunization with Newcastle disease virus (NDV) attenuated vaccine) was established, then the expression characteristics of miR-155 and CTLA-4 gene were analyzed at several key time points during the processes of stress-induced immunosuppression affecting NDV vaccine immune response at serum and tissue levels. The results showed that miR-155 and CTLA-4 were the key factors involved in stress-induced immunosuppression and NDV immune response, whose functions involved in the regulation of immune function were different in different tissues and time points, and 2 day post immunization (dpi), 5dpi and 21dpi were the possible key regulatory time points. CTLA-4, the target gene of miR-155, had significant game regulation relationships between them in various tissues, such as bursa of Fabricius, thymus and liver, indicating that miR-155-CTLA-4 pathway was one of the main mechanisms of their involvement in the regulations of stress-induced immunosuppression affecting NDV immune response. This study can lay the foundation for in-depth exploration of miR-155-CTLA-4 pathway involved in the regulation of immune function.

Transcriptome and metabolome analyses reveal the regulatory effects of compound probiotics on cecal metabolism in heat-stressed broilers

The effect of compound probiotics on the caecum of broilers under heat stress was assessed in this study. A total of 400 twenty-eight-day-old AA male broilers were randomly divided into 4 treatment groups, where each group had 5 replicates of 20 broilers. The 4 treatment groups were a heat stress control group (broilers receiving a normal diet) and groups HP I, HP II, and HP Ⅲ, consisting of broilers receiving 1, 5, and 10 g of compound probiotics added to each kilogram of feed, respectively. Compound probiotics (L. casei, L. acidophilus, and B. lactis at a ratio of 1:1:2) were used to formulate a compound probiotic powder, with 1 × 10¹⁰ CFU/g of effective viable bacteria. Heat stress treatment was performed at 32 ± 1°C from 9:00 to 17:00 every day from 28 d to 42 d. In d 28 to 42, compared with the HC group, the ADG of broilers in the HP II and III groups was significantly increased (P < 0.05); the ADFI difference between groups was not significant (P > 0.05); the FCR of HP II and III broilers was significantly decreased (P < 0.05); and the FCR of the HP I group increased, but the difference was not significant (P > 0.05). Transcriptome results demonstrate that 665 differential genes were screened (DEGs; upregulated: 366, downregulated: 299). The DEGs were enriched in the B cell receptor signaling pathway, the intestinal immune network for IgA synthesis, the Fc epsilon RI signaling pathway, and other signaling pathways, according to KEGG enrichment analysis. Metabolome analysis identified 92 differential metabolites (DAMs; upregulated: 48, downregulated: 44). KEGG enrichment analysis indicated significant enrichment of Pantothenate and CoA biosynthesis and beta-Alanine metabolism. The combined transcriptome and metabolome analysis revealed that the DAMs and DEGs were mostly involved in beta-alanine metabolism, arginine biosynthesis, amino sugar and nucleotide sugar, and alanine, aspartate, and glutamate metabolism. The results of this study suggest that the addition of compound probiotics has a positive effect on intestinal metabolites, improving the growth performance and contributing to the overall health of broilers under heat stress.

Non-Targeted Metabolomic Analysis of Chicken Kidneys in Response to Coronavirus IBV Infection Under Stress Induced by Dexamethasone

Stress in poultry can lead to changes in body metabolism and immunity, which can increase susceptibility to infectious diseases. However, knowledge regarding chicken responses to viral infection under stress is limited. Dexamethasone (Dex) is a synthetic glucocorticoid similar to that secreted by animals under stress conditions, and has been widely used to induce stress in chickens. Herein, we established a stress model in 7-day-old chickens injected with Dex to elucidate the effects of stress on IBV replication in the kidneys. The metabolic changes, immune status and growth of the chickens under stress conditions were comprehensively evaluated. Furthermore, the metabolic profile, weight gain, viral load, serum cholesterol levels, cytokines and peripheral blood lymphocyte ratio were compared in chickens treated with Dex and infected with IBV. An LC-MS/MS-based metabolomics method was used to examine differentially enriched metabolites in the kidneys. A total of 113 metabolites whose abundance was altered after Dex treatment were identified, most of which were lipids and lipid-like molecules. The principal metabolic alterations in chicken kidneys caused by IBV infection included fatty acid, valine, leucine and isoleucine metabolism. Dex treatment before and after IBV infection mainly affected the host’s tryptophan, phenylalanine, amino sugar and nucleotide sugar metabolism. In addition, Dex led to up-regulation of serum cholesterol levels and renal viral load in chickens, and to the inhibition of weight gain, peripheral blood lymphocytes and IL-6 production. We also confirmed that the exogenous cholesterol in DF-1 cells promoted the replication of IBV. However, whether the increase in viral load in kidney tissue is associated with the up-regulation of cholesterol levels induced by Dex must be demonstrated in future experiments. In conclusion, chick growth and immune function were significantly inhibited by Dex. Host cholesterol metabolism and the response to IBV infection are regulated by Dex. This study provides valuable insights into the molecular regulatory mechanisms in poultry stress, and should support further research on the intrinsic link between cholesterol metabolism and IBV replication under stress conditions.

Transcriptome analyses of potential regulators of pre- and post-ovulatory follicles in the pigeon (Columba livia)

To identify the dominant genes controlling follicular maturation, ovulation and regression for pigeon, we used RNA-seq to explore the gene expression profiles of pre- and post-ovulatory follicles of pigeon. We obtained total of 4.73million (96% of the raw data) high-quality clean reads, which could be aligned with 20282 genes. Gene expression profile analysis identified 1461 differentially expressed genes (DEGs) between the pre- (P4) and post-ovulatory follicles (P5). Of these, 843 genes were upregulated, and 618 genes were down-regulated. Furthermore, many DEGs were significantly enriched in some pathways closely related to follicle maturation, ovulation and regression, such as ECM-receptor interaction, vascular smooth muscle contraction, progesterone-mediated oocyte maturation, phagosome. Importantly, the DGEs in ECM-receptor interaction pathway included COL1A1 , COL1A2 , COL4A1 , COL4A2 , ITGA11 , ITGB3 and SDC3 , in the progesterone-mediated oocyte maturation pathway involved CDK1 , CDC25A , CCNB3 , CDC20 and Plk1 , and in the vascular smooth muscle contraction covered CALD1 , KCNMA1 , KCNMB1 , CACNA1 , ACTA2 , MYH10 , MYL3 , MYL6 , MYL9 , closely related to promoting follicular maturation and ovulation in pre-ovulatory follicles. Moreover, it seems that the lysosomal cathepsin family has a decisive role in the regression of early stage of post-ovulatory follicle. Taken together, these data enrich the research of molecular mechanisms of pigeon follicular activities at the transcriptional level and provide novel insight of breeding-related physiology for birds.

The immunotoxicity of decabromodiphenyl ether (BDE-209) on broiler chicks by transcriptome profiling analysis

Decabromodiphenyl ether (BDE-209) has drawn significant attention due to its suppression of immune functions in animals and even humans. In order to explore the mechanism through which BDE-209 affects the immune system, broiler chicks were fed a diet containing various concentrations of BDE-209 (0, 0.004, 0.04, 0.4, and 4 g/kg) for 42 days. Histopathological observations of immune organs found damaged and necrotic lymphocytes in the spleen and bursa, and losses of lymphoid cells in thymic gland. The activities of catalase, glutathione, glutathione peroxidase, and superoxide dismutase in both the spleen and serum were affected by BDE-209. Obvious bioaccumulation effect was found in spleen tissues (high to 1339 ± 181.9 μg/kg). Furthermore, transcriptome sequencing analyses of the spleen identified 424 upregulated and 301 downregulated DEGs, and the cytokine-cytokine receptor interaction signal pathway was most significantly enriched based on the Kyoto Encyclopedia of Genes and Genomes database. Quantitative real-time PCR affirmed the decreased expressions of interleukin IL18, IL18R1, IL18RAP, IL21, as well as interferon gamma IFNG and tumor necrosis factor superfamily members TNFSF8, indicating significant interference to immunomodulation function and possible disease progression in inflammatory effects resulting from BDE-209 exposure. The immunotoxicity of BDE-209 may cause the suppression of immune and physiological functions of spleen cells, leading to inflammation and apoptosis and ultimately spleen atrophy.

Metabolite and transcriptome analyses revealed the modulation of fructo-oligosaccharide on ileum metabolism of Taiping chickens

AIM

The metabolic markers and differentially expressed genes (DEGs) related to fructo-oligosaccharide (FOS) were screened, and the response of FOS to the ileum metabolic pathway of Taiping chickens was analysed.

METHODS AND RESULTS

Prebiotic are widely used in agricultural breeding for care and maintenance of animal health, especially FOS. Metabonomics evaluation of ileum of Taiping chicken ultra-performance liquid chromatography-quadruple time of-flight high-sensitivity mass spectrometry showed that 93 differentially altered metabolites were identified and divided into eight categories, of which organic acids and derivatives was the most important one. Transcriptomic analysis showed that DEGs were mainly enriched in drug metabolism-cytochrome p450, metabolism of xenobiotics by cytochrome p450, retinol metabolism and fat digestion and absorption. Integrated analysis of metabolite profiles and gene expression revealed that the significantly up-regulated GSTT1 was significantly correlated with most of the different lipid metabolites, suggesting that GSTT1 may play an important role in FOS regulation of lipid metabolism.

CONCLUSIONS

The results of this study suggest that supplementation of FOS can have a positive effect on gut metabolites, which may contribute to the overall health with indigenous chickens.

SIGNIFICANCE AND IMPACT OF THE STUDY

Insight into the responses of intestinal prebiotics of Taiping chicken is helpful to understand the role of prebiotics in maintaining intestinal microflora balance and improving immune response and productivity of poultry from the molecular and metabolic levels.

The effectiveness of extended binding affinity of prophage lysin PlyARI against Streptococcus suis infection

Streptococcus suis is an important zoonotic pathogen. An increase in multi-drug-resistant strains has led to poor performance of traditional antibiotic therapies. Thus, alternative antibacterial agents are urgently needed. In this study, we identified a recombined and expressed lysin PlyARI derived from the novel serotype S. suis (Chz) prophage PhiARI0460-1. The recombinant PlyARI at a concentration of 10 µg/mL showed high bacteriolytic activity against 30 S. suis isolates. The minimum inhibitory concentration (MIC) of PlyARI against S. suis was found to be as low as 2 µg/mL, and the lytic efficiency could be maintained between the range of pH 4 and 12. Additionally, in a mouse infection model, a dose of 0.5 mg of PlyARI protected 10 out of 10 mice that were challenged with highly virulent S. suis strain HA9801. Furthermore, the binding specificity of PlyARI was evaluated by constructing a green fluorescent protein (GFP-ARIb), where GFP was fused with the PlyARI-SH3b (cell wall-binding domain, CBD), revealing a high affinity to S. suis, Staphylococcus aureus, and Streptococcus equi along with exhibiting a medium affinity to Streptococcus pneumoniae as well as Streptococcus agalactiae. Overall, our findings indicated that PlyARI may be an alternative antibacterial agent that was useful in treating and possibly the prevention of Streptococcal infections.

Naoxintong restores ischemia injury and inhibits thrombosis via COX2-VEGF/ NFκB signaling

ETHNOPHARMACOLOGICAL RELEVANCE

Naoxintong (NXT) is a traditional Chinese medicine preparation that is often used in combination with aspirin in the treatment of cardiovascular diseases (CVD). One of the main symptoms of CVD is hypoxic-ischemia (HI). The purpose of this study is to find out the molecular nodes targeted by NXT and its related molecular pathways in vascular repair.

MATERIALS AND METHODS

First, human vein umbilical endothelial cells (EA.hy926) were utilized to set up the Oxygen-Glucose Deprivation-Reoxygenation (OGD/R) model and treated with NXT. Cell proliferation, damage and apoptosis were detected by MTT, LDH, and flow cytometry assays. Second, transcriptional responses of OGD/R cells to NXT treatment were investigated. qRT-PCR, western blotting and inhibitor assays were performed. Third, the anti-thrombotic effect of NXT was evaluated by the zebrafish thrombosis model. Morphological observation, histological staining and qRT-PCR assays were implemented on zebrafish model to further observe in vivo the therapeutic effects of NXT on ischemia and thrombosis.

RESULTS

In OGD/R EA.hy926 cells, NXT treatment could reduce ischemic vascular injury, increase cell viability and decrease the proportion of apoptosis. Through RNA-seq analysis, 183 differentially expressed genes (DEGs) were screened with 110 up-regulated genes and 73 down-regulated genes between OGD/R and OGD/R + NXT treated EA.hy926 cells. VEGF and NFκB pathways were enriched. Among these genes, COX2 was identified as one of important targets via which NXT could restore vascular injury. COX2 inhibitor (NS-398), and aspirin, a drug that prevents the development of CVD by targeting COX2, exhibited similar effects to NXT in the treatment of OGD/R EA.hy926 cells. In zebrafish thrombosis model, NXT could attenuate tail venous thrombus and recover the quantity of heart red blood cells. Furthermore, NXT could prevent the formulation of thrombosis and eliminate inflammation in zebrafish by COX2-VEGF/NFκB signaling.

CONCLUSION

Our studies implicated that NXT could restore HI injury and inhibit thrombosis through COX2-VEGF/NFκB signaling, which is consistent with the molecular target of aspirin. This finding might explain the principle of NXT combined with aspirin in the treatment of cardiovascular diseases.

RNA-Seq transcriptome analysis of ileum in Taiping chicken supplemented with the dietary probiotic

Taiping chicken is indigenous chickens (Gallus gallus domesticus), which was one of China's excellent poultry species. As the problems caused by the overuse of antibiotics become more and more concern, people begin to look for ways to replace them. Among them, probiotics and their preparations are the research hotspot to replace antibiotics. Probiotics can promote the absorption of nutrients, improve the ratio of meat to meat, resist and prevent diseases, and improve the intestinal tissue morphology. Here, we performed transcriptome profiling of Taiping chicken ileum which was given probiotics by using the Hiseq™ 2500 sequencing platform. A total of 18 genes were differentially expressed in the ileum under control group and probiotics group. Thirteen genes were upregulated with a range of fold change from 1.02 to 8.61, and 5 were downregulated with a range of fold change from - 1.06 to - 2.29. Ten of the differently expressed genes were further validated by qRT-PCR. In addition, Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that these differentially expressed genes were mainly enriched to bile secretion, alpha-linolenic acid metabolism, linoleic acid metabolism, ether lipid metabolism, and arachidonic acid metabolism. This study will help us to understand the role of probiotics in indigenous chicken production and provide theoretical basis for the genetic development of indigenous chickens.