Genes controlling polyunsaturated fatty acid synthesis are developmentally regulated in broiler chicks

Comprehensive analysis of changes in expression of lncRNA, microRNA and mRNA in liver tissues of chickens with high or low abdominal fat deposition

1. The liver of chickens is a dominant lipid biosynthetic tissue and plays a vital role in fat deposition, particularly in the abdomen. To determine the molecular mechanisms involved in its lipid metabolism, the livers of chickens with high (H) or low (L) abdominal fat content were sampled and sequencing on long non-coding RNA (lncRNA), messenger RNA (mRNA) and small RNA (microRNA) was performed.2. In total, 351 expressed protein-coding genes for long non-coding RNA (DEL; 201 upregulated and 150 downregulated), 400 differentially expressed genes (DEG; 223 upregulated and 177 downregulated) and 10 differentially expressed miRNA (DEM; four upregulated and six downregulated) were identified between the two groups. Multiple potential signalling pathways related to lipogenesis and lipid metabolism were identified via pathway enrichment analysis. In addition, 173 lncRNA - miRNA - mRNA interaction regulatory networks were identified, including 30 lncRNA, 27 mRNA and seven miRNA.3. These networks may help regulate lipid metabolism and fat deposition. Five promising candidate genes and two lncRNA may play important roles in the regulation of adipogenesis and lipid metabolism in chickens.

Hypoxia promotes proliferation and inhibits myogenesis in broiler satellite cells

Breast muscle myopathies in broilers compromise meat quality and continue to plague the poultry industry. Broiler breast muscle myopathies are characterized by impaired satellite cell (SC)-mediated repair, and localized tissue hypoxia and dysregulation of oxygen homeostasis have been implicated as contributing factors. The present study was designed to test the hypothesis that hypoxia disrupts the ability of SC to differentiate and form myotubes, both of which are key components of myofiber repair, and to determine the extent to which effects are reversed by restoration of oxygen tension. Primary SC were isolated from pectoralis major of young (5 d) Cobb 700 chicks and maintained in growth conditions or induced to differentiate under normoxic (20% O2) or hypoxic (1% O2) conditions for up to 48 h. Hypoxia enhanced SC proliferation while inhibiting myogenic potential, with decreased fusion index and suppressed myotube formation. Reoxygenation after hypoxia partially reversed effects on both proliferation and myogenesis. Western blotting showed that hypoxia diminished myogenin expression, activated AMPK, upregulated proliferation markers, and increased molecular signaling of cellular stress. Hypoxia also promoted accumulation of lipid droplets in myotubes. Targeted RNAseq identified numerous differentially expressed genes across differentiation under hypoxia, including several genes that have been associated with myopathies in vivo. Altogether, these data demonstrate localized hypoxia may influence SC behavior in ways that disrupt muscle repair and promote the formation of myopathies in broilers.

Meta-analysis of RNA-Seq datasets highlights novel genes/pathways involved in fat deposition in fat-tail of sheep

Introduction

Fat-tail in sheep is considered as an important energy reservoir to provide energy as a survival buffer during harsh challenges. However, fat-tail is losing its importance in modern sheep industry systems and thin-tailed breeds are more desirable. Using comparative transcriptome analysis to compare fat-tail tissue between fat- and thin-tailed sheep breeds provides a valuable approach to study the complex genetic factors associated with fat-tail development. However, transcriptomic studies often suffer from issues with reproducibility, which can be improved by integrating multiple studies based on a meta-analysis.

Methods

Hence, for the first time, an RNA-Seq meta-analysis on sheep fat-tail transcriptomes was performed using six publicly available datasets.

Results and discussion

A total of 500 genes (221 up-regulated, 279 down-regulated) were identified as differentially expressed genes (DEGs). A jackknife sensitivity analysis confirmed the robustness of the DEGs. Moreover, QTL and functional enrichment analysis reinforced the importance of the DEGs in the underlying molecular mechanisms of fat deposition. Protein-protein interactions (PPIs) network analysis revealed the functional interactions among the DEGs and the subsequent sub-network analysis led to identify six functional sub-networks. According to the results of the network analysis, down-regulated DEGs in green and pink sub-networks (like collagen subunits IV, V, and VI, integrins 1 and 2, SCD, SCD5, ELOVL6, ACLY, SLC27A2, and LPIN1) may impair lipolysis or fatty acid oxidation and cause fat accumulation in tail. On the other hand, up-regulated DEGs, especially those are presented in green and pink sub-networks (like IL6, RBP4, LEPR, PAI-1, EPHX1, HSD11B1, and FMO2), might contribute to a network controlling fat accumulation in the tail of sheep breed through mediating adipogenesis and fatty acid biosynthesis. Our results highlighted a set of known and novel genes/pathways associated with fat-tail development, which could improve the understanding of molecular mechanisms behind fat deposition in sheep fat-tail.

Investigating the role of FADS family members in breast cancer based on bioinformatic analysis and experimental validation

Breast cancer (BC) is the most common malignant tumor in women worldwide. Emerging evidence indicates the significance of fatty acid metabolism in BC. Fatty acid desaturase (FADS) is closely associated with cancer occurrence and development. Here, bioinformatic analysis and experimental validation were applied to investigate the potential functions of FADS in BC. Several public databases, including TCGA, GEO, HPA, Kaplan-Meier plotter, STRING, DAVID, cBioPortal, TIMER, TRRUST, and LinkedOmics were used to determine mRNA/protein expression levels, prognostic significance, functional enrichment, genetic alterations, association with tumor-infiltrating immune cells, and related transcription factors and kinases. BC tissues showed higher and lower mRNA expression of FADS2/6/8 and FADS3/4/5, respectively. FADS1/2/6 and FADS3/4/5 showed higher and lower protein expression levels, respectively, in BC tissues. Moreover, FADS1/7 up- and FADS3/8 down-regulation predicted poor overall and recurrence-free survival, while FADS2/5 up- and FADS4 down-regulation were associated with poor recurrence-free survival. Receiver operating characteristic curves revealed that FADS2/3/4/8 were indicative diagnostic markers. FADS family members showing differential expression levels were associated with various clinical subtypes, clinical stages, lymph node metastasis status, copy number variants, DNA methylation, and miRNA regulation in BC. The mRNA expression level of FADS1/2/3/4/5/7/8 was observed to be significantly negatively correlated with DNA methylation. FADS1/2 upregulation was significantly correlated with clinical stages. FADS1/4 expression was obviously lower in BC patients with higher lymph node metastasis than lower lymph node metastasis, while FADS7/8 expression was obviously higher in BC patients with higher lymph node metastasis than lower lymph node metastasis. FADS family members showed varying degrees of genetic alterations, and Gene Ontology and KEGG pathway enrichment analyses suggested their involvement in lipid metabolism. Their expression level was correlated with immune cell infiltration levels. FADS2 was chosen for further validation analyses. We found FADS2 to be significantly over-expressed in clinical BC tissue samples. The proliferation, migration, and invasion abilities of MDA-MB-231 and BT474 cells were significantly reduced after FADS2 knockdown. Furthermore, FADS2 may promote the occurrence and development of BC cells via regulating the epithelial-mesenchymal transition (EMT) pathway. Altogether, our results suggest that FADS1/2/3/4 can serve as potential therapeutic targets, prognostic indicators, and diagnostic markers in patients with BC.

Technical note: an optimized method to isolate, purify, and differentiate satellite cells from broiler chicks

Development and maintenance of healthy muscle fibers rely on the myogenic potential of satellite cells (SC), muscle stem cells that proliferate and differentiate to form myotubes. Satellite cells are indispensable for post-hatch muscle growth as well as muscle repair and regeneration when myofibers are damaged. Pectoralis major of young broiler chicks (5-d olds) is a readily available source of SC, which can be used in vitro to elucidate cellular and molecular mechanisms responsible for muscle growth and regeneration in broilers. Here, we optimized a method for efficient isolation, purification, and differentiation of SC, from young broiler chicks. This procedure includes a simple method that allows SC to be purified from other muscle cell types that can impede the fidelity of follow-on experiments, particularly highly sensitive measures such as RNAseq. The methods for culturing and differentiating SC into multinucleated myotubes were also optimized by testing serum types, concentrations, and the effects of chicken embryo extract. Using the isolation procedure, a highly pure SC population (94.6 ± 2.11% Pax7+) with high viability and yield was obtained, and their capacity to differentiate into myotubes was confirmed. Enrichment for SC and myogenic capacity were maintained through multiple passages and after cryopreservation. Analysis of gene expression over the first 48 h of differentiation confirmed that SC exhibited the expected molecular signature of myogenesis. Taken together, this method simplifies the ability to isolate and maintain a relatively pure population of SC with strong myogenic potential from young broiler chicks, and should support downstream applications for assessing the impact of nutrients, metabolites, and other physiological cues on muscle growth and development in broilers.

The effects of maternal fish oil supplementation rich in n-3 PUFA on offspring-broiler growth performance, body composition and bone microstructure

This study evaluated the effects of maternal fish oil supplementation rich in n-3 PUFA on the performance and bone health of offspring broilers at embryonic development stage and at market age. Ross 708 broiler breeder hens were fed standard diets containing either 2.3% soybean oil (SO) or fish oil (FO) for 28 days. Their fertilized eggs were collected and hatched. For a pre-hatch study, left tibia samples were collected at 18 days of incubation. For a post-hatch study, a total of 240 male chicks from each maternal treatment were randomly selected and assigned to 12 floor pens and provided with the same broiler diets. At 42 days of age, growth performance, body composition, bone microstructure, and expression of key bone marrow osteogenic and adipogenic genes were evaluated. One-way ANOVA was performed, and means were compared by student’s t-test. Maternal use of FO in breeder hen diet increased bone mineral content (p < 0.01), bone tissue volume (p < 0.05), and bone surface area (p < 0.05), but decreased total porosity volume (p < 0.01) during the embryonic development period. The FO group showed higher body weight gain and feed intake at the finisher stage than the SO group. Body composition analyses by dual-energy X-ray absorptiometry showed that the FO group had higher fat percentage and higher fat mass at day 1, but higher lean mass and total body mass at market age. The decreased expression of key adipogenic genes in the FO group suggested that prenatal FO supplementation in breeder hen diet suppressed adipogenesis in offspring bone marrow. Furthermore, no major differences were observed in expression of osteogenesis marker genes, microstructure change in trabecular bone, or bone mineral density. However, a significant higher close pores/open pores ratio suggested an improvement on bone health of the FO group. Thus, this study indicates that maternal fish oil diet rich in n-3 PUFA could have a favorable impact on fat mass and skeletal integrity in broiler offspring.

Endometrial gene expression in response to lipopolysaccharide between estrous cycle phases and uterine horns in cattle

Uterine bacterial community abundances shift throughout the estrous cycle, potentially altering the immunological environment of the uterus and impacting subsequent fertility. The objective of the current study was to evaluate the immunological impact of lipopolysaccharide (LPS), as a model for potentially pathogenic bacteria, throughout the uterine endometrium between the luteal and follicular phase of the estrous cycle. Bovine uterine tracts were harvested in mid-luteal (n = 7) or follicular (n = 7) phase. Explants were collected from the contralateral and ipsilateral horn relative to the dominant follicle or corpus luteum, then subjected to one of three treatments: uncultured control, cultured control, or cultured with LPS (1 µg/mL). Explants underwent RNA extraction and targeted RNA sequencing for expression analyses of 40 immune response related genes. Sequencing reads were mapped to Bos taurus genome in CLC Genomics Workbench. Resulting total read counts were normalized by housekeeping gene GAPDH and analyzed for overall expression profile by Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA) and Variable Importance in Projection (VIP) analyses in Metaboanalyst. Individual gene expression differences were determined by GLIMMIX procedure in SAS with fixed effects of treatment, estrous phase, uterine horn, and their interaction, with random effect of individual uterus. Expression of 29 genes were affected among treatment groups, with seven genes increased in LPS treatment compared to other groups (P &lt; 0.05). Multiple genes were affected by estrous phase and uterine horn, independent of treatment (P &lt; 0.05). The OPLS-DA analyses indicated overall gene expression differences due to clustering by estrous cycle and treatment (P &lt; 0.001), with no effect of uterine horn (P &gt; 0.10). Similar clustering was observed between luteal and follicular phase explants of controls, but distinct separate clustering between phases with LPS treatment (P = 0.001). According to VIP analyses, mucins were identified as contributing the most to differences observed between phase and treatment. In conclusion, estrous cycle phase resulted in differing overall endometrial gene expression profiles of immune response to LPS treatment. Therefore, altered immunological environment of the uterus in response to bacteria at different estrous cycle stages may lead to differences in reproductive success.

Breast Meat Fatty Acid Profiling and Proteomic Analysis of Beijing-You Chicken During the Laying Period

The disparity in fatty acids (FA) composition exhibits a significant impact on meat quality, however, the molecular regulatory mechanisms underlying this trait in chicken are far from clear. In this study, a total of 45 female Beijing-You chicken (BYC) hens, fed on the same diet, were collected at the slaughter age of 150, 300, or 450 days (D150, D300, and D450) from sexual maturation stage to culling stage (15 birds per age). Gas chromatography-mass spectrometry (GC-MS) and tandem mass tag labeling technology based on liquid chromatography mass spectrometry (TMT-LC-MS/MS) analysis strategies were applied to profile FA compositions and to compare differential expressed proteins (DEPs) between these different slaughter ages, respectively. The FA profiling showed that increasing hen ages resulted in increased contents of both saturated and unsaturated fatty acids. Proteomic analyses showed a total of 4,935 proteins in chicken breast muscle with the false discovery rate (FDR) < 1% and 664 of them were differentially expressed (fold change > 1.50 or < 0.67 and P < 0.01). There were 410 up- and 116 down-regulated proteins in D150 vs. D300 group, 32 up- and 20 down-regulated in D150 vs. D450 group, and 72 up- and 241 down-regulated in D300 vs. D450 group. A total of 57 DEPs related to FA/lipid-related metabolisms were obtained according to the enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). These DEPs were involved in 21 significantly enriched (P < 0.05) pathways, including well-known pathways for FA synthesis (metabolism, desaturation, and elongation) and the signaling pathways for lipid metabolism (PPAR, adipocytokine, calcium, VEGF, MAPK, and Wnt). In addition, there existed several representative DEPs (FABP, FABP3, apoA-I, apoA-IV, apoC-III, apoB, VTG1, and VTG2) involved in the regulation of FA/lipid transportation. The construction of the interaction networks indicated that HADH, ACAA2, HADHA, ACSL1, CD36, CPT1A, PPP3R1, and SPHK1 were the key core nodes. Finally, eight DEPs were quantified using parallel reaction monitoring (PRM) to validate the results from TMT analysis. These results expanded our understanding of how the laying age affects the FA compositions and metabolism in hen breast meat.

A selected population study reveals the biochemical mechanism of intramuscular fat deposition in chicken meat

BACKGROUND

Increasing intramuscular fat (IMF) is an important strategy to improve meat quality, but the regulation mechanism of IMF deposition needs to be systematically clarified.

RESULTS

A total of 520 chickens from a selected line with improved IMF content and a control line were used to investigate the biochemical mechanism of IMF deposition in chickens. The results showed that the increased IMF would improve the flavor and tenderness quality of chicken meat. IMF content was mainly determined both by measuring triglyceride (TG) and phospholipid (PLIP) in muscle tissue, but only TG content was found to be decisive for IMF deposition. Furthermore, the increase in major fatty acid (FA) components in IMF is mainly derived from TGs (including C16:0, C16:1, C18:1n9c, and C18:2n6c, etc.), and the inhibition of certain very-long-chain FAs would help to IMF/TG deposition.

CONCLUSIONS

Our study elucidated the underlying biochemical mechanism of IMF deposition in chicken: Prevalent accumulation of long-chain FAs and inhibitions of medium-chain FAs and very long chain FA would jointly result in the increase of TGs with the FA biosynthesis and cellular uptake ways. Our findings will guide the production of high-quality chicken meat.

Fighting Fat With Fat: n-3 Polyunsaturated Fatty Acids and Adipose Deposition in Broiler Chickens

Modern broiler chickens are incredibly efficient, but they accumulate more adipose tissue than is physiologically necessary due to inadvertent consequences of selection for rapid growth. Accumulation of excess adipose tissue wastes feed in birds raised for market, and it compromises well-being in broiler-breeders. Studies driven by the obesity epidemic in humans demonstrate that the fatty acid profile of the diet influences adipose tissue growth and metabolism in ways that can be manipulated to reduce fat accretion. Omega-3 polyunsaturated fatty acids (n-3 PUFA) can inhibit adipocyte differentiation, induce fatty acid oxidation, and enhance energy expenditure, all of which can counteract the accretion of excess adipose tissue. This mini-review summarizes efforts to counteract the tendency for fat accretion in broilers by enriching the diet in n-3 PUFA.

Identification of the molecular regulation of differences in lipid deposition in dedifferentiated preadipocytes from different chicken tissues

BACKGROUND

A body distribution with high intramuscular fat and low abdominal fat is the ideal goal for broiler breeding. Preadipocytes with different origins have differences in terms of metabolism and gene expression. The transcriptome analysis performed in this study of intramuscular preadipocytes (DIMFPs) and adipose tissue-derived preadipocytes (DAFPs) aimed to explore the characteristics of lipid deposition in different chicken preadipocytes by dedifferentiation in vitro.

RESULTS

Compared with DAFPs, the total lipid content in DIMFPs was reduced (P < 0.05). Moreover, 72 DEGs related to lipid metabolism were screened, which were involved in adipocyte differentiation, fatty acid transport and fatty acid synthesis, lipid stabilization, and lipolysis. Among the 72 DEGs, 19 DEGs were enriched in the PPAR signaling pathway, indicating its main contribution to the regulation of the difference in lipid deposition between DAFPs and DIMFPs. Among these 19 genes, the representative APOA1, ADIPOQ, FABP3, FABP4, FABP7, HMGCS2, LPL and RXRG genes were downregulated, but the ACSL1, FABP5, PCK2, PDPK1, PPARG, SCD, SCD5, and SLC27A6 genes were upregulated (P < 0.05 or P < 0.01) in the DIMFPs. In addition, the well-known pathways affecting lipid metabolism (MAPK, TGF-beta and calcium) and the pathways related to cell communication were enriched, which may also contribute to the regulation of lipid deposition. Finally, the regulatory network for the difference in lipid deposition between chicken DAFPs and DIMFPs was proposed based on the above information.

CONCLUSIONS

Our data suggested a difference in lipid deposition between DIMFPs and DAFPs of chickens in vitro and proposed a molecular regulatory network for the difference in lipid deposition between chicken DAFPs and DIMFPs. The lipid content was significantly increased in DAFPs by the direct mediation of PPAR signaling pathways. These findings provide new insights into the regulation of tissue-specific fat deposition and the optimization of body fat distribution in broilers.

Profiling of RNA N 6 -Methyladenosine Methylation Reveals the Critical Role of m6A in Chicken Adipose Deposition

One of the main objectives of broiler breeding is to prevent excessive abdominal adipose deposition. The role of RNA modification in adipose deposition is not clear. This study was aimed to map m⁶A modification landscape in chicken adipose tissue. MeRIP-seq was performed to compare the differences in m⁶A methylation pattern between fat and lean broilers. We found that start codons, stop codons, coding regions, and 3′-untranslated regions were generally enriched for m⁶A peaks. The high m⁶A methylated genes (fat birds vs. lean birds) were primarily associated with fatty acid biosynthesis and fatty acid metabolism, while the low m⁶A methylated genes were mainly involved in processes associated with development. Furthermore, we found that the mRNA levels of many genes may be regulated by m⁶A modification. This is the first comprehensive characterization of m⁶A patterns in the chicken adipose transcriptome, and provides a basis for studying the role of m⁶A modification in fat deposition.