scholarly journals Transcriptional Insights into Key Genes and Pathways Underlying Muscovy Duck Subcutaneous Fat Deposition at Different Developmental Stages

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 2099
Author(s):  
Liping Guo ◽  
Congcong Wei ◽  
Li Yi ◽  
Wanli Yang ◽  
Zhaoyu Geng ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Fatty Acid Biosynthesis ◽  
Developmental Stages ◽  
Subcutaneous Fat ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Muscovy Duck ◽  
Key Genes

Subcutaneous fat is a crucial trait for waterfowl, largely associated with meat quality and feed conversion rate. In this study, RNA-seq was used to identify differentially expressed genes of subcutaneous adipose tissue among three developmental stages (12, 35, and 66 weeks) in Muscovy duck. A total of 138 and 129 differentially expressed genes (DEGs) were identified between 35 and 12 weeks (wk), and 66 and 35 wk, respectively. Compared with 12 wk, subcutaneous fat tissue at 35 wk upregulated several genes related to cholesterol biosynthesis and fatty acid biosynthesis, including HSD17B7 and MSMO1, while it downregulated fatty acid beta-oxidation related genes, including ACOX1 and ACSL1. Notably, most of the DEGs (92.2%) were downregulated in 66 wk compared with 35 wk, consistent with the slower metabolism of aging duck. Protein network interaction and function analyses revealed GC, AHSG, FGG, and FGA were the key genes for duck subcutaneous fat from adult to old age. Additionally, the PPAR signaling pathway, commonly enriched between the two comparisons, might be the key pathway contributing to subcutaneous fat metabolism among differential developmental stages in Muscovy duck. These results provide several candidate genes and pathways potentially involved in duck subcutaneous fat deposition, expanding our understanding of the molecular mechanisms underlying subcutaneous fat deposition during development.

scholarly journals Transcriptome analysis of miRNA and mRNA in the livers of pigs with highly diverged backfat thickness

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kai Xing ◽  
Xitong Zhao ◽  
Hong Ao ◽  
Shaokang Chen ◽  
Ting Yang ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Energy Metabolism ◽  
Differentially Expressed Genes ◽  
Regulatory Network ◽  
Acid Synthesis ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Backfat Thickness ◽  
Lipid Deposition ◽  
Differentially Expressed Mirnas

AbstractFat deposition is very important in pig production, and its mechanism is not clearly understood. MicroRNAs (miRNAs) play critical roles in fat deposition and energy metabolism. In the current study, we investigated the mRNA and miRNA transcriptome in the livers of Landrace pigs with extreme backfat thickness to explore miRNA-mRNA regulatory networks related to lipid deposition and metabolism. A comparative analysis of liver mRNA and miRNA transcriptomes from pigs (four pigs per group) with extreme backfat thickness was performed. We identified differentially expressed genes from RNA-seq data using a Cufflinks pipeline. Seventy-one differentially expressed genes (DEGs), including twenty-eight well annotated on the porcine reference genome genes, were found. The upregulation genes in pigs with higher backfat thickness were mainly involved in fatty acid synthesis, and included fatty acid synthase (FASN), glucokinase (GCK), phosphoglycerate dehydrogenase (PHGDH), and apolipoprotein A4 (APOA4). Cytochrome P450, family 2, subfamily J, polypeptide 34 (CYP2J34) was lower expressed in pigs with high backfat thickness, and is involved in the oxidation of arachidonic acid. Moreover, 13 differentially expressed miRNAs were identified. Seven miRNAs were associated with fatty acid synthesis, lipid metabolism, and adipogenic differentiation. Based on comprehensive analysis of the transcriptome of both mRNAs and miRNAs, an important regulatory network, in which six DEGs could be regulated by differentially expressed miRNAs, was established for fat deposition. The negative correlate in the regulatory network including, miR-545-5p and GRAMD3, miR-338 and FASN, and miR-127, miR-146b, miR-34c, miR-144 and THBS1 indicate that direct suppressive regulation may be involved in lipid deposition and energy metabolism. Based on liver mRNA and miRNA transcriptomes from pigs with extreme backfat thickness, we identified 28 differentially expressed genes and 13 differentially expressed miRNAs, and established an important miRNA-mRNA regulatory network. This study provides new insights into the molecular mechanisms that determine fat deposition in pigs.

scholarly journals RNA-Seq Reveals Differentially Expressed Genes and Pathways Affecting Intramuscular Fat Metabolism in Huangshan Black Chicken Population

2020 ◽  
Vol 12 (3) ◽  
pp. 117
Author(s):  
S. H. Yang ◽  
C. S. He ◽  
C. H. Li ◽  
G. Q. Liu
Keyword(s):  
Fatty Acid ◽  
Candidate Genes ◽  
Meat Quality ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Interaction Network ◽  
Intramuscular Fat ◽  
Metabolic Process ◽  
Differentially Expressed ◽  
Thigh Muscle

Intramuscular fat (IMF) plays an important role in meat quality due to its positive correlation with juiciness, tenderness, and flavor. However, for chickens, the molecular mechanisms underlying IMF deposition in thigh muscle have not yet been determined. Here, to identify candidate genes and signaling pathways related to IMF deposition, we deeply explored the chicken transcriptome from thigh muscles of Huangshan Black Chickens with extremely high and low phenotypic values for intramuscular fat content. A total of 128 genes differentially expressed genes (DEGs) were detected, of which 94 were up-regulated and 34 were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways revealed these DEGs (including FABP4, G0S2, PLIN1, SCD1, LFABP, SLC1A6, SLC45A3, ACSBG1, LY86, ST8SIA5, SNAI2, HPGD, EDN2, and THRSP) were significantly enriched in lipid biosynthetic process, steroid biosynthetic and metabolic process, fatty acid metabolic process, and regulation of unsaturated fatty acid metabolic pathways. Additionally, we concluded an interaction network related to lipid metabolism, which might be contributed to the IMF deposition in chicken. Overall, we proposed some new candidate genes and interaction networks that can be associated with IMF deposition and used as biomarkers in meat quality improvement.

scholarly journals Comparative adipose transcriptome analysis digs out genes related to fat deposition in two pig breeds

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kai Xing ◽  
Kejun Wang ◽  
Hong Ao ◽  
Shaokang Chen ◽  
Zhen Tan ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Signaling Pathway ◽  
Meat Quality ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Mapk Signaling ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Pig Breeds

Abstract Fatness traits are important in pigs because of their implications for fattening efficiency, meat quality, reproductive performance and immunity. Songliao black pigs and Landrace pigs show important differences in production and meat quality traits, including fatness and muscle growth. Therefore, we used a high-throughput massively parallel RNA-seq approach to identify genes differentially expressed in backfat tissue between these two breeds (six pigs in each). An average of 37.87 million reads were obtained from the 12 samples. After statistical analysis of gene expression data by edgeR, a total of 877 differentially expressed genes were detected between the two pig breeds, 205 with higher expression and 672 with lower expression in Songliao pigs. Candidate genes (LCN2, CES3, DGKB, OLR1, LEP, PGM1, PCK1, ACACB, FADS1, FADS2, MOGAT2, SREBF1, PPARGC1B) with known effects on fatness traits were included among the DEGs. A total of 1071 lncRNAs were identified, and 85 of these lncRNAs were differentially expressed, including 53 up-regulated and 32 down-regulated lncRNAs, respectively. The differentially expressed genes and lncRNAs involved in glucagon signaling pathway, glycolysis/gluconeogenesis, insulin signaling pathway, MAPK signaling pathway and so on. Integrated analysis potential trans-regulating or cis-regulating relation between DEGs and DE lncRNAs, suggested lncRNA MSTRG.2479.1 might regulate the expressed level of VLDLR affecting porcine fat metabolism. These results provide a number of candidate genes and lncRNAs potentially involved in porcine fat deposition and provide a basis for future research on the molecular mechanisms underlying in fat deposition.

scholarly journals Analysis of molecular mechanism for acceleration of polyembryony using gene functional annotation pipeline in Copidosoma floridanum

2020 ◽  
Author(s):  
Takuma Sakamoto ◽  
Maaya Nishiko ◽  
Hidemasa Bono ◽  
Takeru Nakazato ◽  
Jin Yoshimura ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Interaction ◽  
Functional Annotation ◽  
Molecular Mechanisms ◽  
Fatty Acid Biosynthesis ◽  
Interaction Analysis ◽  
Differentially Expressed ◽  
Control Group ◽  
Copidosoma Floridanum ◽  
Human Genes

Abstract Background: Polyembryony is defined as the formation of several embryos from a single egg. This phenomenon can occur in humans, armadillo, and some endoparasitoid insects. However, the mechanism underlying polyembryogenesis in animals remains to be elucidated. The polyembryonic parasitoid wasp Copidosoma floridanum oviposits its egg into an egg of the host insect; eventually, over 2,000 individuals will arise from one egg. Previously, we reported that polyembryogenesis is enhanced when the juvenile hormone (JH) added to the culture medium in the embryo culture. Hence, in the present study, we performed RNA sequencing (RNA-Seq) analysis to investigate the molecular mechanisms controlling polyembryogenesis of C. floridanum . Functional annotation of genes is not fully available for C.floridanum ; however, whole genome assembly has been archived. Hence, we constructed a pipeline for gene functional annotation in C. floridanum and performed molecular network analysis. We analyzed differentially expressed genes between control and JH-treated molura after 48 h of culture, then used the tblastx program to assign whole C. floridanum transcripts to human gene. Results: We obtained 11,117 transcripts in the JH treatment group and identified 217 differentially expressed genes compared with the control group. As a result, 76% of C. floridanum transcripts were assigned to human genes. Gene enrichment analysis revealed genes associated with platelet degranulation, fatty acid biosynthesis, cell morphogenesis in the differentiation and integrin signaling pathways were fluctuated following JH treatment. Furthermore, Cytoscape analysis revealed a molecular interaction that was possibly associated with polyembryogenesis . Conclusions: We have constructed a pipeline for gene functional annotation of C. floridanum , and identified transcripts with high similarity to human genes during early embryo developmental. Additionally, this study reveals new molecular interactions associated with polyembryogenesis; these interactions could indicate the molecular mechanisms underlying polyembryony. Our results highlight the potential utility of molecular interaction analysis in human twins.

Identification of key factors associated with early- and late-onset ovarian serous cystadenocarcinoma

2020 ◽  
Vol 16 (34) ◽  
pp. 2821-2833
Author(s):  
Shuang Ma ◽  
Yang Zheng ◽  
Chengwei Fei
Keyword(s):  
Overall Survival ◽  
Differentially Expressed Genes ◽  
Early Onset ◽  
Molecular Mechanisms ◽  
Late Onset ◽  
Differentially Expressed ◽  
Key Factors ◽  
Factors Associated ◽  
Serous Cystadenocarcinoma ◽  
Key Genes

Aim: To uncover the molecular mechanisms of early-onset ovarian serous cystadenocarcinoma (EOOSC; patients <50 years old) and late-onset ovarian serous cystadenocarcinoma (LOOSC; patients ≥50 years old). Materials & methods: Bioinformatics was utilized to identify the key factors. Results: 478 EOOSC and 899 LOOSC individual differentially expressed genes were identified and enriched in different pathways. The expression of key genes LAG3, LRRC63 and MT1B significantly influenced the overall survival of EOOSC patients. The expression of key genes RDH12, NTSR1, ZSCAN16, CT45A3 and EPPIN_WFDC6 significantly affected the overall survival of LOOSC patients. Conclusions: The molecular mechanisms of EOOSC and LOOSC appear to be different, so that patients might be treated individually in respect of age.

scholarly journals Identification of Differentially Expressed Genes and Pathways for Abdominal Fat Deposition in Ovariectomized and Sham-Operated Chickens

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 155 ◽  
Author(s):  
Xiaopeng Mu ◽  
Xiaoyan Cui ◽  
Ranran Liu ◽  
Qinghe Li ◽  
Maiqing Zheng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Abdominal Fat ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Feed Conversion ◽  
Fat Percentage ◽  
Steroid Biosynthesis

Ovariectomy results in improved meat quality (growth rate, tenderness, and flavor) of broilers. However, some negative effects increased (abdominal fat (AF) deposition, low feed conversion, etc.) have also been reported. In this study, the gene expression profiles of AF tissue in ovariectomized and sham-operated chickens were determined to identify differentially expressed genes (DEGs) and pathways to explore the molecular mechanisms underlying AF accumulation. Comparing the ovariectomized group and the sham-operated group, the abdominal fat weight (AFW) and abdominal fat percentage (AFP) were increased significantly (p < 0.05) at 14 and 19 weeks after ovariectomy. According to the gene expression profiling analysis, 108 DEGs of fat metabolism were screened from 1461 DEGs. Among them, ABCA1, ABCACA, LPL, CREB1, PNPLA2, which are involved in glycerolipid—or steroid—associated biological processes, and the hormone receptor genes, ESR1 and PRLR, were down-regulated significantly in the ovariectomized group compared to the sham-operated group (p < 0.05). Conversely, CETP, DGAT2, DHCR24, HSD17B7 and MSMO1, were significantly up-regulated (p < 0.05) after ovariectomy. Based on the DEGs, the glycerolipid metabolism, steroid biosynthesis, and other signaling pathways (MAPK, TGF-β, and adhesion pathways, etc.) were enriched, which may also contribute to the regulation of AF deposition. Our data suggest that AF deposition was significantly increased in ovariectomized chickens by the down-regulation of the decomposition genes of glycerolipid metabolism, which inhibits AF degradation, and the up-regulation of steroid biosynthesis genes, which increases fat accumulation. These findings provide new insights into the molecular mechanisms of fat deposition in the ovariectomized chickens.

scholarly journals Identification of key genes for HNSCC from public databases using bioinformatics analysis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yuchu Ye ◽  
Jingyi Wang ◽  
Faya Liang ◽  
Pan Song ◽  
Xiaoqing Yan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Survival Analysis ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
The Cancer Genome Atlas ◽  
Differentially Expressed ◽  
Apical Plasma Membrane ◽  
Bioinformatics Analyses ◽  
Oncomine Database ◽  
Key Genes

Abstract Background The cause and underlying molecular mechanisms of head and neck squamous cell carcinoma (HNSCC) are unclear. Our study aims to identify the key genes associated with HNSCC and reveal potential biomarkers. Methods In this study, the expression profile dataset GSE83519 of the Gene Expression Omnibus database and the RNA sequencing dataset of HNSCC of The Cancer Genome Atlas were included for analysis. Sixteen differentially expressed genes were screened from these two datasets using R software. Gene Expression Profiling Interactive Analysis 2 (GEPIA2) was then adopted for survival analysis, and finally, three key genes related to the overall survival of HNSCC patients were identified. Furthermore, we verified these three genes using the Oncomine database and from real-time PCR and immunohistochemistry results from HNSCC tissues. Results The expression data of 44 samples from GSE83519 and 545 samples from TCGA-HNSC were collected. Using bioinformatics, the two databases were integrated, and 16 DEGs were screened out. Gene Ontology (GO) enrichment analysis showed that the biological functions of DEGs focused primarily on the apical plasma membrane and regulation of anoikis. Kyoto Encyclopedia of Genes and Genomes (KEGG) signalling pathway analysis showed that these DEGs were mainly involved in drug metabolism-cytochrome P450 and serotonergic synapses. Survival analysis identified three key genes, CEACAM5, CEACAM6 and CLCA4, that were closely related to HNSCC prognosis. The Oncomine database, qRT–PCR and IHC verified that all 3 key genes were downregulated in most HNSCC tissues compared to adjacent normal tissues. Conclusions This study indicates that integrated bioinformatics analyses play an important role in screening for differentially expressed genes and pathways in HNSCC, helping us better understand the biomarkers and molecular mechanism of HNSCC.

scholarly journals Pan-transcriptomic analysis identified common differentially expressed genes of Acinetobacter baumannii in response to polymyxin treatments

2020 ◽  
Vol 16 (4) ◽  
pp. 327-338
Author(s):  
Mengyao Li ◽  
Su Mon Aye ◽  
Maizbha Uddin Ahmed ◽  
Mei-Ling Han ◽  
Chen Li ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Acinetobacter Baumannii ◽  
Outer Membrane ◽  
Differentially Expressed Genes ◽  
Fatty Acid Biosynthesis ◽  
Efflux Pumps ◽  
Transcriptomic Analysis ◽  
Differentially Expressed ◽  
Acid Biosynthesis

Our pan-transcriptomic study for polymyxin-treated A. baumannii identified that the remodelled outer membrane, up-regulated efflux pumps and down-regulated fatty acid biosynthesis might be essential for early responses to polymyxins in A. baumannii.

scholarly journals Comparative analysis of gene expression profiles in differentiated subcutaneous adipocytes between Jiaxing Black and Large White pigs

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Dawei Zhang ◽  
Wenjing Wu ◽  
Xin Huang ◽  
Ke Xu ◽  
Cheng Zheng ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Differentially Expressed Genes ◽  
Expression Profiles ◽  
Subcutaneous Fat ◽  
Mapk Signaling ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Large White ◽  
Pig Breeds

Abstract Background Chinese domestic pig breeds are reputed for pork quality, but their low ratio of lean-to-fat carcass weight decreases production efficiency. A better understanding of the genetic regulation network of subcutaneous fat tissue is necessary for the rational selection of Chinese domestic pig breeds. In the present study, subcutaneous adipocytes were isolated from Jiaxing Black pigs a Chinese indigenous pig breed with redundant subcutaneous fat deposition and Large White pigs a lean-type pig breed with relatively low subcutaneous fat deposition. The expression profiles of mRNAs and lncRNAs were compared by RNA-seq analysis to identify biomarkers correlated with the differences of subcutaneous fat deposition between the two breeds. Results A total of 1058 differentially expressed genes and 221 differentially expressed lncRNAs were identified in subcutaneous adipocytes between Jiaxing Black and Large White pigs, which included 275 up-regulated mRNAs, 783 down-regulated mRNAs, 118 up-regulated lncRNAs and 103 down-regulated lncRNAs. Gene Ontology and KEGG pathway enrichment analyses revealed that the differentially expressed genes and differentially expressed lncRNAs were mainly involved in the immune response, cell fate determination, PI3K-Akt signaling pathway and MAPK signaling pathway, which are known to be related to adipogenesis and lipid metabolism. The expression levels of differentially expressed genes and differentially expressed lncRNAs according to the RNA-seq data were verified by quantitative PCR, which showed 81.8% consistency. The differences in MAPK pathway activity between Jiaxing Black and Large White pigs was confirmed by western blot analysis, which revealed elevated p38 phosphorylation in Jiaxing Black pigs. Conclusions This study offers a detailed characterization of mRNAs and lncRNAs in fat- and lean-type pig breeds. The activity of the MAPK signaling pathway was found to be associated with subcutaneous adipogenesis. These results provide new targets for further investigation of the molecular mechanisms regulating subcutaneous fat deposition in pigs.

Identification of Differentially Expressed Genes Associated with Papillary Thyroid Carcinoma

2020 ◽  
Vol 23 (6) ◽  
pp. 546-553
Author(s):  
Hongyuan Cui ◽  
Mingwei Zhu ◽  
Junhua Zhang ◽  
Wenqin Li ◽  
Lihui Zou ◽  
...  
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Cellular Proliferation ◽  
Mrna Level ◽  
Thyroid Tissue ◽  
Differentially Expressed ◽  
Thyroid Tumors ◽  
Papillary Thyroid

Objective: Next-generation sequencing (NGS) was performed to identify genes that were differentially expressed between normal thyroid tissue and papillary thyroid carcinoma (PTC). Materials & Methods: Six candidate genes were selected and further confirmed with quantitative real-time polymerase chain reaction (qRT-PCR), and immunohistochemistry in samples from 24 fresh thyroid tumors and adjacent normal tissues. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was used to investigate signal transduction pathways of the differentially expressed genes. Results: In total, 1690 genes were differentially expressed between samples from patients with PTC and the adjacent normal tissue. Among these, SFRP4, ZNF90, and DCN were the top three upregulated genes, whereas KIRREL3, TRIM36, and GABBR2 were downregulated with the smallest p values. Several pathways were associated with the differentially expressed genes and involved in cellular proliferation, cell migration, and endocrine system tumor progression, which may contribute to the pathogenesis of PTC. Upregulation of SFRP4, ZNF90, and DCN at the mRNA level was further validated with RT-PCR, and DCN expression was further confirmed with immunostaining of PTC samples. Conclusion: These results provide new insights into the molecular mechanisms of PTC. Identification of differentially expressed genes should not only improve the tumor signature for thyroid tumors as a diagnostic biomarker but also reveal potential targets for thyroid tumor treatment.

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