RNA sequencing reveals lncRNA-mediated non-mendelian inheritance of feather growth change in chickens.

BACKGROUND: Long non-coding RNAs (lncRNAs) play an essential role in biological processes. However, the expression patterns of lncRNAs that regulate the non-Mendelian inheritance feather phenotypes remain unknown. OBJECTIVE: This study aimed to compare the expression profiles of lncRNAs in the follicles of the late-feathering cocks (LC) and late-feathering hens (LH) that followed genetic rules and the early-feathering hen (EH) and early-feathering cock (EC) that did not conform to the genetic laws. METHODS: We performed RNA sequencing and investigated the differentially expressed lncRNAs (DElncRNAs) between the early- and late-feathering chickens, which function by cis-acting or participate in the competing endogenous RNA (ceRNA) network. RESULTS: A total of 53 upregulated and 43 downregulated lncRNAs were identified in EC vs. LC, and 58 upregulated and 109 downregulated lncRNAs were identified in EH vs. LH. The target mRNAs regulated by lncRNAs in cis were enriched in the pentose phosphate pathway, TGF-ß signaling pathway and Jak-STAT signaling pathway in EC vs. LC and were associated with the TGF-ß signaling pathway, Wnt signaling pathway, p53 signaling pathway and Jak-STAT signaling pathway in EH vs. LH. In addition, the lncRNA-mediated ceRNA regulatory pathways of hair follicle formation were mainly enriched in the TGF-ß signaling pathway, Wnt signaling pathway, melanogenesis, and calcium signaling pathways. The levels of ENSGALG00000047626 were significantly higher in the late-feathering chickens than in the early-feathering chickens, which regulated the expression of SSTR2 by gga-miR-1649-5p. CONCLUSION: This study provides a novel molecular mechanism of lncRNA's response to the feather rate that does not conform to the genetic laws in chickens.

Transcriptome sequencing reveals genes involved in cadmium-triggered oxidative stress in the chicken heart.

As a ubiquitous heavy metal, cadmium (Cd) is highly toxic to various organs. However, the effects and molecular mechanism of Cd toxicity in the chicken heart remain largely unknown. The goal of our study was to investigate the cardiac injury in chickens' exposure to Cd. We detected the levels of oxidative stress-related molecules in the Cd-induced chicken heart, and assessed the histopathological changes by hematoxylin and eosin staining. RNA sequencing was performed to identify differentially expressed mRNAs between the Cd-induced group and control group. The expression of candidate genes involved in oxidative stress was certified by quantitative reverse transcription PCR. Our results showed that the expression of glutathione, peroxidase, and superoxide dismutase was significantly decreased and malondialdehyde was increased in the heart of chickens by Cd induction. The disorderly arranged cardiomyocytes, swelled and enlarged cells, partial cardiomyocyte necrosis, blurred morphological structure, and notable inflammatory cell infiltration were observed in the Cd-induced chicken heart. RNA sequencing identified 23 upregulated and 11 downregulated mRNAs in the heart tissues of the chicken in the Cd-induced group, and functional pathways indicated that they were associated with oxidative stress. Moreover, CREM, DUSP8, and ITGA11 expressions were significantly reduced, whereas LAMA1 expression was induced in heart tissue of chickens by Cd treatment. Overall, our findings revealed that oxidative stress and pathological changes in the chicken heart could be triggered by Cd. The mRNA transcriptional profiles identified differentially expressed genes in the chicken heart by Cd induction, revealing oxidative stress-related key genes and enhancing our understanding of Cd toxicity in the chicken heart.

Long Non-coding RNA Expression Profile in Broiler Liver with Cadmium-Induced Oxidative Damage.

Cadmium pollution is serious heavy metal pollution in environmental pollution and impacts on livestock productivity. However, the effect and mechanisms of cadmium toxicity on the broiler remain unclear. This study aimed to explore the liver oxidative damage and reveal the related long non-coding RNA (lncRNA) expression patterns in the broiler liver with cadmium exposure. The broilers were fed with diets containing CdCl2 and detected the oxidative stress indexes in the liver tissues. Transcriptome sequencing of broiler liver was performed to identify cadmium exposure-related differentially expressed lncRNAs (DElncRNAs). The functions and pathways of DElncRNAs were analyzed by GO and KEGG. The sequencing results were verified by the quantitative real-time polymerase chain reaction. Cadmium exposure induced tissue structure disorder, focal hemorrhage, and irregular hepatocytes in the broiler liver, and significantly decreased GSH level and enzyme activities, and increased MDA expression in the liver. A total of 74 DElncRNAs were obtained in cadmium group compared with the control group, which were enriched in the GO terms, including intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator, branched-chain amino acid biosynthetic process. The enriched KEGG pathways, including lysine biosynthesis, valine, leucine and isoleucine biosynthesis, and pantothenate and CoA biosynthesis, were related to oxidative stress. PCR analysis indicated that the changes in ENSGALG00000053559, ENSGALG00000053926, and ENSGALG00000054404 expression were consistent with sequencing. Our results provide novel lncRNAs involved in oxidative stress in the broiler liver with cadmium exposure.

Peroxisome proliferator-activated receptor-coactivator 1-beta (PGC-1ß) modulates the expression of genes involved in adipogenesis during preadipocyte differentiation in chicken.

To study the influence of the PGC-1ß gene on chicken adipocyte proliferation and differentiation, we constructed RNA interference (RNAi) vectors that target the PGC-1ß gene and transfected these vectors into adipocytes. Oil Red O staining and a CCK-8 cell kit were used to determine cell triglyceride accumulation status and cell proliferation after transfection, respectively. The mRNA abundances of PGC-1ß and adipocyte-differentiation-related genes (PPARγ, C/EBPα, SREBP-1c, FAS, and A-FABP) were detected by real-time PCR. The results showed that the mRNA and protein abundances of PGC-1ß in PGC-1ß-shRNA transfected adipocytes were significantly lower than those in the control. Interference decreased cell differentiation, but did not depress the cell proliferation. PGC-1ß interference impeded the triglyceride accumulation, the mRNA expression levels of nuclear receptors PPARγ and SREBP-1c, and fatty acid synthetase (FAS), and both proteins PPARγ and SREBP-1c, and the fatty acids transporting protein A-FABP. Generally, PGC-1ß modulated the cell differentiation and triglyceride accumulation in chicken adipocytes.

Genotypes of IFIH1 and IFIT5 in seven chicken breeds indicated artificial selection for commercial traits influenced antiviral genes.

Innate immunity is the first line against the invasion of pathogenic microorganisms. Previous reports only demonstrated production traits of commercial importance were often negatively correlated with innate disease resistance. However, whether different purpose of artificial selection influences innate immunity have not been understood. In this study, we cloned exon1, exon6 of IFIH1 and exon2 of IFIT5 by molecular biology techniques in seven different chicken breeds to detect the potential effect of artificial selection for commercial traits on disease resistance for the first time. In total, 8 single nucleotide polymorphisms(SNPs) of IFIH1 gene exon1 and exon6, 19 SNPs of IFIT5 gene exon2 were detected. We found all native chicken breeds had a relatively close relationship to broiler breeds but a remote relationship to layer breed. A great difference between CB and LLH with different selected purpose were observed. The allele frequencies of these two positive antiviral genes were associated with different purpose of artificial selection. Our experiment constituted the foundation for the interaction between commercial traits and immune trait.

Feasibility and value of quantitative dynamic contrast enhancement MR imaging in the evaluation of sinonasal tumors.

BACKGROUND: Quantitative dynamic contrast enhancement MR imaging (DCE-MRI), used to measure properties of tissue microvasculature and tumor angiogenesis, is a promising method for distinguishing benign and malignant tumors and characterizing tumor response to antiangiogenic treatment. The aim of this study was to assess the feasibility of quantitative parameters derived from clinically used DCE-MRI for distinguishing benign from malignant tumors in the sinonasal area, which may be potentially useful for prediction and monitoring of treatment response to chemoradiotherapy of sinonasal tumors. METHODS: One hundred and forty-three patients with sinonasal tumors, including 78 malignant tumors and 65 benign tumors and tumor-like lesions, underwent clinically used DCE-MRI. Parametric maps were obtained for quantitative parameters including K(trans), kep and ve. Two radiologists reviewed these maps and measured K(trans), kep and ve in the tumor tissue. Data were analyzed using independent T-test or Mann-Whitney U test analysis and receiver operating characteristic curves. RESULTS: K(trans), kep and ve showed significant differences between benign and malignant tumors in the sinonasal area (P = 0.000 1). The accuracy of K(trans), kep and ve in differentiation between benign and malignant sinonasal tumors were 72.0%, 76.2% and 67.1%, respectively. There were significant differences in kep and ve between malignant epithelial sinonasal tumors and lymphomas (P < 0.05). Using a ve value of 0.213 as the threshold value differentiated malignant epithelial tumors from lymphomas with an accuracy of 78.3%, sensitivity of 88.2%, specificity of 68.0%, positive predictive value of 66.7%, and negative predictive value of 90.9%. However, no significant difference in K(trans) and kep was found between malignant epithelial and non-epithelial tumors in the sinonasal area (P > 0.05). CONCLUSIONS: It is feasible that quantitative parameters of tumors can be derived from clinically used DCE-MRI in the sinonasal region. Preliminary findings suggest an increased value for quantitative DCE-MRI in the evaluation of sinonasal tumors in clinical practice.

A comparison of arterial spin labeling perfusion MRI and DCE-MRI in human prostate cancer.

Perfusion MRI has the potential to provide pathophysiological biomarkers for the evaluating, staging and therapy monitoring of prostate cancer. The objective of this study was to explore the feasibility of noninvasive arterial spin labeling (ASL) to detect prostate cancer in the peripheral zone and to investigate the correlation between the blood flow (BF) measured by ASL and the pharmacokinetic parameters K(trans) (forward volume transfer constant), kep (reverse reflux rate constant between extracellular space and plasma) and ve (the fractional volume of extracellular space per unit volume of tissue) measured by dynamic contrast-enhanced (DCE) MRI in patients with prostate cancer. Forty-three consecutive patients (ages ranging from 49 to 86 years, with a median age of 74 years) with pathologically confirmed prostate cancer were recruited. An ASL scan with four different inversion times (TI = 1000, 1200, 1400 and 1600 ms) and a DCE-MRI scan were performed on a clinical 3.0 T GE scanner. BF, K(trans), kep and ve maps were calculated. In order to determine whether the BF values in the cancerous area were statistically different from those in the noncancerous area, an independent t-test was performed. Spearman's bivariate correlation was used to assess the relationship between BF and the pharmacokinetic parameters K(trans), kep and ve. The mean BF values in the cancerous areas (97.1 ± 30.7, 114.7 ± 28.7, 102.3 ± 22.5, 91.2 ± 24.2 ml/100 g/min, respectively, for TI = 1000, 1200, 1400, 1600 ms) were significantly higher (p < 0.01 for all cases) than those in the noncancerous regions (35.8 ± 12.5, 42.2 ± 13.7, 53.5 ± 19.1, 48.5 ± 13.5 ml/100 g/min, respectively). Significant positive correlations (p < 0.01 for all cases) between BF and the pharmacokinetic parameters K(trans), kep and ve were also observed for all four TI values (r = 0.671, 0.407, 0.666 for TI = 1000 ms; 0.713, 0.424, 0.698 for TI = 1200 ms; 0.604, 0.402, 0.595 for TI = 1400 ms; 0.605, 0.422, 0.548 for TI = 1600 ms). It can be seen that the quantitative ASL measurements show significant differences between cancerous and benign tissues, and exhibit strong to moderate correlations with the parameters obtained using DCE-MRI. These results show the promise of ASL as a noninvasive alternative to DCE-MRI.

[Association between single nucleotide polymorphism of ADFP gene and carcass traits and intramuscular fat content in chicken].

In order to investigate the effect of ADFP gene on the carcass traits and intramuscular fat content of Da-heng high-quality chicken, we analyzed the coding sequence of the ADFP gene by single-strand conformation polymorphism (SSCP) and DNA sequencing in five pure lines and three crossbreds. We found three single nucleotide polymorphism sites, including A/T at base position 4,079 (locus A), C/T at base position 4,843 (locus B) and A/G at base position 7,070 (locus C). GLM analysis for the effect of genotypes on carcass traits and intramuscular fat content demonstrated a significant effect on leg muscle percentage, abdomen fat weight, abdominal fat percentage and intra-muscular fat content in locus A (P < 0.05), a significant association with living body weight and carcass weight for locus B (P < 0.05) and a significant association with breast muscle weight and intramuscular fat content (P < 0.05), and a very significant association with breast muscle percentage for locus C (P < 0.01). It was concluded that ADFP gene may be a major gene or linked to such a gene that affects the fat traits of birds. Polymorphic loci A and C could be used as molecular markers for abdominal fat weight, abdominal fat percentage and intramuscular fat content in birds in future studies.