The AMPK signaling pathway is associated with the intramuscular fat trait in pigs

Background. Intramuscular fat (IMF) is an important economic trait for pork quality and a complex quantitative trait regulated by multiple genes. The objective of this work was to investigate the novel transcriptional effects of a multigene pathways on IMF deposition in the longissimus dorsi(LD) muscles of pigs. Methods. Potential signaling pathways were screened by mining data from three gene expression profiles in the GEO database. We designed quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) arrays for the candidate signaling pathways to verify the results in the LD muscles of three pig breeds with different IMF contents(Large White, Berkshire and Min). Results. The AMPK signaling pathway was screened via bioinformatic analysis. Ten key hub genes of this signaling pathway(AMPK, ADIPOR1, ADIPOR2, LKB1, CAMKKβ, CPT1A, CPT1B, PGC-1α, CD36 and ACC1) were differentially expressed. Statistical analyses revealed that AMPK pathway activity clearly varied among the three pig breeds. Conclusion. Based on these results, we concluded that the activation of the AMPK signaling pathway plays a positive role in reducing IMF deposition in pigs.

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The AMPK signaling pathway is associated with the intramuscular fat trait in pigs

10.7287/peerj.preprints.26976v1 ◽

2018 ◽

Author(s):

Chaogang Yao ◽

Daxin Pang ◽

Chao Lu ◽

Aishi Xu ◽

Peixuan Huang ◽

...

Keyword(s):

Signaling Pathways ◽

Signaling Pathway ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Bioinformatic Analysis ◽

Intramuscular Fat ◽

Large White ◽

Positive Role ◽

Ampk Signaling ◽

Pig Breeds

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Data Mining and Validation of AMPK Pathway as a Novel Candidate Role Affecting Intramuscular Fat Content in Pigs

Animals ◽

10.3390/ani9040137 ◽

2019 ◽

Vol 9 (4) ◽

pp. 137 ◽

Cited By ~ 1

Author(s):

Chaogang Yao ◽

Daxin Pang ◽

Chao Lu ◽

Aishi Xu ◽

Peixuan Huang ◽

...

Keyword(s):

Gene Expression ◽

Western Blot ◽

Signaling Pathways ◽

Signaling Pathway ◽

Blot Analysis ◽

Western Blot Analysis ◽

Intramuscular Fat ◽

Large White ◽

Ampk Signaling ◽

Pig Breeds

Intramuscular fat (IMF) is an important economic trait for pork quality and a complex quantitative trait regulated by multiple genes. The objective of this work was to investigate the novel transcriptional effects of a multigene pathway on IMF deposition in the longissimus dorsi (LD) muscles of pigs. Potential signaling pathways were screened by mining data from three gene expression profiles in the Gene Expression Omnibus (GEO) database. We designed quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) arrays for the candidate signaling pathways to verify the results in the LD muscles of two pig breeds with different IMF contents (Large White and Min). Western blot analysis was used to detect the expression levels of several candidate proteins. Our results showed that the AMPK signaling pathway was screened via bioinformatics analysis. Ten key hub genes of this signaling pathway (AMPK, ADIPOR1, ADIPOR2, LKB1, CAMKKβ, CPT1A, CPT1B, PGC-1α, CD36, and ACC1) were differentially expressed between the Large White and Min pigs. Western blot analysis further confirmed that LKB1/CaMKK2-AMPK-ACC1-CPT1A axis dominates the activity of AMPK signaling pathway. Statistical analyses revealed that AMPK signaling pathway activity clearly varied among the two pig breeds. Based on these results, we concluded that the activation of the AMPK signaling pathway plays a positive role in reducing IMF deposition in pigs.

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

10.21203/rs.3.rs-19837/v1 ◽

2020 ◽

Author(s):

Dawei Zhang ◽

Wenjing Wu ◽

Xin Huang ◽

Ke Xu ◽

Cheng Zheng ◽

...

Keyword(s):

Signaling Pathway ◽

Expression Profiles ◽

Mapk Signaling ◽

Fat Deposition ◽

Mapk Signaling Pathway ◽

Differentially Expressed ◽

Rna Seq ◽

Domestic Pig ◽

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 SC fat tissue is necessary for the rational selection of Chinese domestic pig breeds. In the present study, SC adipocytes were isolated from Jiaxing Black pigs (a Chinese indigenous pig breed with redundant SC fat deposition) and Large White pigs (a lean-type pig breed with relatively low SC fat deposition) and the expression profiles of mRNAs and lncRNAs were compared by RNA-seq analysis to identify biomarkers correlated with the differences of SC fat deposition between the two breeds.Results: A total of 3,371 differentially expressed genes (DEGs) and 1,182 differentially expressed lncRNAs (DELs) were identified in SC adipocytes between Jiaxing Black (JX) and Large White (LW) pigs, which included 797 upregulated mRNAs, 2,574 downregulated mRNAs, 461 upregulated lncRNAs and 721 downregulated lncRNAs. Gene Ontology and KEGG pathway analyses revealed that the DEGs and DELs 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 DEGs and DELs according to the RNA-seq data were verified by quantitative PCR, which showed 81.8% consistency. The differences in MAPK pathway activity between JX and LW pigs was confirmed by western blot analysis, with <100-fold elevated p38 phosphorylation in JX 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 greatly enhance our understanding of the molecular mechanisms regulating SC fat deposition in pigs.

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Genome-Wide Analysis of mRNAs and lncRNAs of Intramuscular Fat Related to Lipid Metabolism in Two Pig Breeds

Cellular Physiology and Biochemistry ◽

10.1159/000495101 ◽

2018 ◽

Vol 50 (6) ◽

pp. 2406-2422 ◽

Cited By ~ 2

Author(s):

Wanlong Huang ◽

Xiuxiu Zhang ◽

Ai Li ◽

Lingli Xie ◽

Xiangyang Miao

Keyword(s):

Lipid Metabolism ◽

Lipid Accumulation ◽

Expression Profiles ◽

Intramuscular Fat ◽

Fat Deposition ◽

Differentially Expressed ◽

Regulation Mechanism ◽

Large White ◽

Pig Breeds ◽

Significant Difference

Background/Aims: Long non-coding RNAs (lncRNAs) can regulate adipogenesis and lipid accumulation. Intramuscular fat deposition appears to vary in different pig breeds, and the regulation mechanism has not yet been fully elucidated at molecular level. Moreover, little is known about the function and profile of lncRNAs in intramuscular fat deposition and metabolism in pig. The aim of this study was thus to explore the regulatory functions of lncRNAs in intramuscular fat deposition. Methods: In this study, Laiwu (LW) pig and Large White (LY) pig with significant difference in fat deposition were selected for use. RNA-seq technology and bioinformatics methods were used to comparatively analyze the gene expression profiles of intramuscular fat between LW and LY pigs to identify key mRNAs and lncRNAs associated with lipid metabolism and adipogenesis. Real-time fluorescence-based quantitative PCR was applied to verify the expression level of the differentially expressed mRNAs and lncRNAs. Results: A total of 513 mRNAs and 55 lncRNAs were differentially expressed between two pig breeds. By co-expression network construction as well as cis- and trans-regulated target gene analysis, 31 key lncRNAs were identified. Gene Ontology and KEGG pathway analyses revealed that differentially expressed genes and lncRNAs were mainly involved in the biological processes and pathways related to adipogenesis and lipid metabolism. Conclusion: XLOC_046142, XLOC_004398 and XLOC_015408 may target MAPKAPK2, NR1D2 and AKR1C4, respectively, and play critical regulatory roles in intramuscular adipogenesis and lipid accumulation in pig. XLOC_064871 and XLOC_011001 may play a role in lipid metabolism-related disease via regulating TRIB3 and BRCA1. This study provides a valuable resource for lncRNA study and improves our understanding of the biological roles of lipid metabolism- related genes and molecular mechanism of intramuscular fat metabolism and deposition.

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

BMC Genomics ◽

10.1186/s12864-020-07361-9 ◽

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.

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Association between leptin receptor gene polymorphism and quality of both meat and back fat in large white pigs of ukrainian breeding

Agricultural science and practice ◽

10.15407/agrisp3.02.042 ◽

2016 ◽

Vol 3 (2) ◽

pp. 42-48

Author(s):

V. Balatsky ◽

I. Bankovska ◽

A. Saienko

Keyword(s):

Gene Polymorphism ◽

Leptin Receptor ◽

Receptor Gene ◽

Intramuscular Fat ◽

Large White ◽

Pig Breeds ◽

Lepr Gene ◽

Large White Breed ◽

White Breed

Leptin receptor is one of the components of the system of regulating energy homeostasis of the organism. Leptin receptor gene (LEPR) polymorphism is associated with pig carcass index of the content of intramus- cular fat in its valuable parts, which is particularly important when assessing the quality of their carcasses for processing. Intramuscular fat is associated with meat fl avor characteristics and partly determines its tenderness, juiciness, and other parameters. Aim. To analyze LEPR gene (SNP NM001024587.1, p. 1987 C > T) polymor- phism in populations of various pig breeds and to establish its relationship with the quality of both meat and fat of pigs of Large White breed of Ukrainian breeding. Methods. Genetic-population analysis of nine pig breeds, associative analysis on the search connection of LEPR gene polymorphism with quality of both meat and fat of pigs of Large White breed of Ukrainian breeding. LEPR locus genotyping was performed by High Resolution Melting (HRM). Results. All the studied breeds are characterized by polymorphism of the leptin receptor gene (SNP NM001024587.1, p. 1987 C > T), signifi cant breed specifi city in the distribution of frequencies of alleles was established. Statistically confi rmed effect (p < 0.05) of genotypes LEPR on the content of intramuscular fat, total dry matter and moisture in the meat, as well as the moisture content in the back fat of pigs of Ukrainian Large White breed was revealed. Higher content of intramuscular fat was found in the animals with genotype TT, while a smaller amount of intramuscular fat and more moisture in fat was revealed in heterozygotes. Conclusions. Genetic marker LEPR SNP NM001024587.1, p. 1987 C > T can be used in the marker-assisted selection to predict and improve the performance quality of the meat of pigs of Large White breed of the Ukrainian breeding. These results suggest that porcine leptin receptor gene controls the quality of fat comp- lex – inside muscles and in the dorsal part of the carcass.

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Gene Expression Profiles Associated with Radio-Responsiveness in Locally Advanced Rectal Cancer

Biology ◽

10.3390/biology10060500 ◽

2021 ◽

Vol 10 (6) ◽

pp. 500

Author(s):

Jeeyong Lee ◽

Junhye Kwon ◽

DaYeon Kim ◽

Misun Park ◽

KwangSeok Kim ◽

...

Keyword(s):

Candidate Genes ◽

Expression Profiles ◽

Cell Cycle Control ◽

Methylation Status ◽

Locally Advanced ◽

Gene Expression Profiles ◽

Advanced Rectal Cancer ◽

Bioinformatic Analysis ◽

Locally Advanced Rectal Cancer ◽

Genes Encoding

LARC patients were sorted according to their radio-responsiveness and patient-derived organoids were established from the respective cancer tissues. Expression profiles for each group were obtained using RNA-seq. Biological and bioinformatic analysis approaches were used in deciphering genes and pathways that participate in the radio-resistance of LARC. Thirty candidate genes encoding proteins involved in radio-responsiveness–related pathways, including the immune system, DNA repair and cell-cycle control, were identified. Interestingly, one of the candidate genes, cathepsin E (CTSE), exhibited differential methylation at the promoter region that was inversely correlated with the radio-resistance of patient-derived organoids, suggesting that methylation status could contribute to radio-responsiveness. On the basis of these results, we plan to pursue development of a gene chip for diagnosing the radio-responsiveness of LARC patients, with the hope that our efforts will ultimately improve the prognosis of LARC patients.

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PSIV-6 Differential gene expression of fibro/adipogenic progenitors between Wagyu and Brahman cattle: A possible contribution to their different meat quality

Journal of Animal Science ◽

10.1093/jas/skab235.553 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 301-301

Author(s):

Chaoyang Li ◽

Qianglin Liu ◽

Matt Welborn ◽

Leshan Wang ◽

Yuxia Li ◽

...

Keyword(s):

Gene Expression ◽

Skeletal Muscle ◽

Meat Quality ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Cattle Breed ◽

Intramuscular Fat ◽

Brahman Cattle ◽

Differential Gene ◽

The Difference

Abstract The amount of intramuscular fat directly influences the meat quality. However, significant differences in the ability to accumulate intramuscular fat are present among different beef cattle breeds. While Wagyu, a cattle breed that originated from Japan, is renowned for abundant intramuscular fat, Brahman cattle generally have very little intramuscular fat accumulation and produce tougher meat. We identified that bovine intramuscular fat is derived from a group of bipotent progenitor cells named fibro/adipogenic progenitors (FAPs) which also give rise to fibroblasts. Thus, the variation in intramuscular fat development between Wagyu and Brahman is likely attributed to the difference in FAPs between these two breeds. In order to understand the gene expression difference between FAPs of the two breeds, single-cell RNA-seq was performed using total single-nucleated cells isolated from the longissimus muscle of young purebred Wagyu, purebred Brahman, and Wagyu-Brahman cross cattle. FAPs constitute the largest single-nucleated cell population in both Wagyu and Brahman skeletal muscle. Multiple subpopulations of FAPs with different gene expression profiles were identified, suggesting that FAP is a heterogeneous population. A unique FAP cluster expressing lower levels of fibrillar collagen and extracellular remodeling enzyme genes but higher levels of select proadipogenic genes was identified exclusively in Wagyu skeletal muscle, which likely contributes to the robust intramuscular adipogenic efficiency of Wagyu FAPs. In conclusion, the difference in the cellular composition and gene expression of FAPs between Wagyu and Brahman cattle likely contribute to their distinct meat quality.

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