Deep sequencing microRNA profiles associated with wooden breast in commercial broilers

Integrated analysis of miRNA and mRNA expression profiles associated with wooden breast myopathy in broiler chickens

Wooden breast (WB) myopathy has raised a worldwide concern among broiler industry during the past decade. Despite progress in understanding its etiology from transcriptional regulation, post-transcriptional mechanisms including the regulation of microRNAs (miRNAs) remain largely unknown. In the current study, we described an integrative analysis between mRNA and miRNA expression profiles of pectoralis major muscle from normal and WB myopathic broilers. A total of 1983 differentially expressed mRNAs (DEmRNAs) and 155 DEmiRNAs were identified in WB. We screened crucial biological processes and core DEmRNAs enriched in functional pathways, and established the protein-protein interaction network. DEmiRNAs and negatively correlated DEmRNAs regulatory networks were constructed, including 44 exist DEmiRNAs and 478 DEmRNAs, forming 772 miRNA-mRNA pairs. Upregulated DEmiRNAs including gga-miR-21-3p, gga-miR-460a-5p and gga-miR-6631-5p, as well as downregulated DEmiRNAs including gga-miR-182-5p, gga-miR-183 and gga-miR-96-5p were identified as hub miRNAs. Meanwhile, functional enrichment analysis indicated that upregulated DEmRNAs in the network were enriched in biological processes of response to stimulus, inflammatory response, extracellular matrix organization, whereas downregulated DEmRNAs were enriched in carbohydrate, amino acid and nucleotide metabolic processes. Collectively, our integrative miRNA and mRNA analysis highlighted candidate miRNAs and mRNAs, as well as potential miRNA-mRNA regulatory mechanisms involved in WB myopathy in broiler chicken.

Exploration and practice of potential association prediction between diseases and drugs based on Swanson framework and bioinformatics

Compared to traditional intermediate concepts, specific bioinformatics entities are more informative and higher directional. This study is based on the BITOLA system and combines bioinformatics methods to determine the intermediate concept which is key to improve efficiency of Literature-based Knowledge Discovery, proposes the concept of "Swanson framework + Bioinformatics", and conducts practice of Literature-based Knowledge Discovery to improve the scientificity and efficiency of research and development. Firstly, detected the disease related genes (i.e. differentially expressed genes) according to the results of gene functional analysis as intermediate concepts to carry out Literature-based Knowledge Discovery. Taking the disease "Autism Spectrum Disorder (ASD)" as an example, the potential "disease-drug" association was predicted, and the predicted drugs were verified from the perspective of bioinformatics. Two drugs potentially associated with ASD were found: Fish oil and Forskolin, which were closely related to ASD in bioinformatics analysis results and literature verification. The two "disease-drug" association results showed better scientificity. The BIOINF-ABC+ model improves the accuracy of calculations by 76% compared to using the BITOLA system alone. In addition, it also shows high accuracy and credibility in literature verification. The BIOINF-ABC+ model based on the "Swanson framework + Bioinformatics" has good practicality, applicability, and accuracy in conducting "disease-drug" association prediction in the biomedical field, and can be used for mining "disease-drug" relationships.

Differential expression of miRNAs associated with pectoral myopathies in young broilers: insights from a comparative transcriptome analysis

INTRODUCTION

White Striping (WS) and Wooden Breast (WB) pectoral myopathies are relevant disorders for contemporary broiler production worldwide. Several studies aimed to elucidate the genetic components associated with the occurrence of these myopathies. However, epigenetic factors that trigger or differentiate these two conditions are still unclear. The aim of this study was to identify miRNAs differentially expressed (DE) between normal and WS and WB-affected broilers, and to verify the possible role of these miRNAs in metabolic pathways related to the manifestation of these pectoral myopathies in 28-day-old broilers.

RESULTS

Five miRNAs were DE in the WS vs control (gga-miR-375, gga-miR-200b-3p, gga-miR-429-3p, gga-miR-1769-5p, gga-miR-200a-3p), 82 between WB vs control and 62 between WB vs WS. Several known miRNAs were associated with WB, such as gga-miR-155, gga-miR-146b, gga-miR-222, gga-miR-146-5p, gga-miR- 29, gga-miR-21-5p, gga-miR-133a-3p and gga-miR-133b. Most of them had not previously been associated with the development of this myopathy in broilers. We also have predicted 17 new miRNAs expressed in the broilers pectoral muscle. DE miRNA target gene ontology analysis enriched 6 common pathways for WS and WB compared to control: autophagy, insulin signaling, FoxO signaling, endocytosis, and metabolic pathways. The WS vs control contrast had two unique pathways, ERBB signaling and the mTOR signaling, while WB vs control had 14 unique pathways, with ubiquitin-mediated proteolysis and endoplasmic reticulum protein processing being the most significant.

CONCLUSIONS

We found miRNAs DE between normal broilers and those affected with breast myopathies at 28 days of age. Our results also provide novel evidence of the miRNAs role on the regulation of WS and in the differentiation of both WS and WB myopathies. Overall, our study provides insights into miRNA-mediated and pathways involved in the occurrence of WS and WB helping to better understand these chicken growth disorders in an early age. These findings can help developing new approaches to reduce these complex issues in poultry production possibly by adjustments in nutrition and management conditions. Moreover, the miRNAs and target genes associated with the initial stages of WS and WB development could be potential biomarkers to be used in selection to reduce the occurrence of these myopathies in broiler production.

Time course evaluation of collagen type IV in Pectoralis major muscles of broiler chickens selected for different growth-rates

Collagen type IV (COL4) is one of the major components of animals' and humans' basement membranes of several tissues, such as skeletal muscles and vascular endothelia. Alterations in COL4 assembly and secretion are associated to muscular disorders in humans and animals among which growth-related abnormalities such as white striping and wooden breast affecting Pectoralis major muscles (PMs) in modern fast-growing (FG) chickens. Considering the high prevalence of these myopathies in FG broilers and that a worsening is observed as the bird slaughter age is increased, the present study was intended to evaluate the distribution and the expression level of COL4 protein and its coding genes in PMs of FG broilers at different stages of muscle development (i.e., 7, 14, 21, 28, 35, and 42 d of age). Medium-growing (MG) chickens have been considered as the control group in consideration of the lower selection pressure on breast muscle growth rate and hypertrophy. Briefly, 5 PM/sampling time/genotype were selected for western blot, immunohistochemistry (IHC), and gene expression analyses. The normalized expression levels of COL4 coding genes showed an overexpression of COL4A2 in FG than MG at d 28, as well as a significant decrease in its expression over their rearing period. Overall, results obtained through the gene expression analysis suggested that selection for the hypertrophic growth of FG broilers may have led to an altered regulation of fibroblast proliferation and COL4 synthesis. Moreover, western blot and IHC analyses suggested an altered secretion and/or degradation of COL4 protein in FG broilers, as evidenced by the fluctuating trend of 2 bands observed in FG over time. In view of the above, the present research supports the evidence about a potential aberrant synthesis and/or degradation of COL4 and corroborates the hypothesis regarding a likely involvement of COL4 in the series of events underlying the growth-related abnormalities in modern FG broilers.

Multi-omics reveals the mechanisms underlying Lactiplantibacillus plantarum P8-mediated attenuation of oxidative stress in broilers challenged with dexamethasone

Oxidative stress is a common phenomenon in poultry production. Several molecules, including antioxidant genes, miRNAs, and gut microbiota metabolites, have been reported to participate in redox regulation. Lactiplantibacillus plantarum P8 (P8) was shown to improve the antioxidant capacity of chickens, but the specific molecular mechanisms remain unclear. In this study, 400 broilers were allocated to 4 treatment groups: control diet (Con group), control diet + dexamethasone injection (DEX group), control diet containing 1 × 108 CFU/g P8 (P8 group), and control diet containing 1 × 108 CFU/g P8 + DEX injection (DEX_P8 group). Integrated analysis of the microbiome, metabolomics, and miRNAomics was conducted to investigate the roles of P8 in oxidative stress in broilers. Results demonstrated that P8 supplementation significantly improved growth performance, jejunal morphology, and antioxidant function in DEX-treated broilers. Analysis of the gut microbiota revealed a higher abundance of Barnesiella (P = 0.01) and Erysipelatoclostridium (P = 0.05) in the DEX_P8 group than in the DEX group. Functional prediction indicated that certain pathways, including the phenylacetate degradation pathway, were enriched in the DEX_P8 group compared to the DEX group. Metabolites in the cecal contents were distinct between the groups. P8 supplementation increased the content of metabolites with antioxidant capacity, e.g., urobilinogen (P < 0.01), and decreased that of metabolites related to oxidative stress, e.g., genistein (P < 0.01). Functional prediction indicated that metabolites that differed between the DEX_P8 and DEX groups were enriched in pathways including "tryptophan metabolism" and "primary bile acid biosynthesis". The miRNAomics analysis further showed that, compared to the DEX group, several miRNAs in the jejunum, such as gga-miR-21-3p (P = 0.03), were increased, whereas gga-miR-455-3p (P = 0.02) was decreased in the DEX_P8 group. The PI3K-Akt, Ras, and Rap1 signaling pathways were enriched in the DEX_P8 group compared to the DEX group through KEGG analysis. Correlation analysis revealed potential interactions between growth performance, oxidation/antioxidation, jejunal morphology, gut microbiota, cecal content metabolites, and jejunal miRNAs. Overall, our results indicate that P8 supplementation may improve the growth performance, jejunal morphology and antioxidant capacity of DEX-treated broilers by regulating gut microbiota, its metabolites, and intestinal miRNAs.

hsa-mir-(4328, 4422, 548z and -628-5p) in diabetic retinopathy: diagnosis, prediction and linking a new therapeutic target

AIMS

Growing evidence suggests that microRNAs (miRNAs) are crucial in controlling how diabetic retinopathy (DR) develops. We intend to mine miRNAs with diagnostic and predictive value for DR and to investigate new drug therapeutic targets.

METHODS

After performing a differential analysis on the miRNA and mRNA datasets for DR and neovascularization (NEO), miRNA-mRNA networks were created. Combine the results of enrichment analysis, Protein-Protein Interaction Networks (PPI), and Cytoscape to identify key miRNAs. DrugBank was used to find drugs that interacted with transcription factors (TF) predicted by TransmiR. Finally, whole blood and clinical data were collected from 58 patients with type 2 diabetes mellitus (T2DM), and RT-qPCR, logistic analysis, and ROC were used to verify the value of key miRNAs.

RESULTS

Differential analysis indicated the presence of genes and miRNAs that co-regulate DR and NEO. Enrichment analysis showed that key genes are inextricably linked to neovascularization. Combining the results of PPI and Cytoscape identified four key miRNAs, namely hsa-mir-(4328, 4422, 548z and -628-5p). RT-qPCR, logistic, and ROC results showed that decreased expression levels of hsa-mir-(4328, 4422, 548z and -628-5p) signal the risk of evolution to DR in T2DM patients. Finally, we constructed a TF-miRNA network to find the 15 TFs and the 35 drugs that interact with these TFs.

CONCLUSION

hsa-mir-(4328, 4422, 548z and -628-5p) in whole blood are protective factors for DR as novel biomarkers for diagnosis and prediction. In addition, our research provides new drug directions for the treatment of DR, such as Diosmin, Atorvastatin, and so on.