Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Jan 25:14:1053021.
doi: 10.3389/fgene.2023.1053021. eCollection 2023.

RNA-seq transcriptome profiling of pigs' liver in response to diet with different sources of fatty acids

Simara Larissa Fanalli  1 , Bruna Pereira Martins da Silva  2 , Julia Dezen Gomes  2 , Mariah Castro Durval  1 , Vivian Vezzoni de Almeida  3 , Gabriel Costa Monteiro Moreira  4 , Bárbara Silva-Vignato  2 , Juliana Afonso  5 , Felipe André Oliveira Freitas  2 , James Mark Reecy  6 , James Eugene Koltes  6 , Dawn Koltes  6 , Dorian Garrick  7 , Luciana Correia de Almeida Regitano  5 , Júlio Cesar de Carvalho Balieiro  8 , Gerson Barreto Mourão  2 , Luiz Lehmann Coutinho  2 , Heidge Fukumasu  1 , Severino Matias de Alencar  2 , Albino Luchiari Filho  2 , Aline Silva Mello Cesar  1   2
Affiliations

RNA-seq transcriptome profiling of pigs' liver in response to diet with different sources of fatty acids

Simara Larissa Fanalli et al. Front Genet. .

Abstract

Pigs (Sus scrofa) are an animal model for metabolic diseases in humans. Pork is an important source of fatty acids (FAs) in the human diet, as it is one of the most consumed meats worldwide. The effects of dietary inclusion of oils such as canola, fish, and soybean oils on pig gene expression are mostly unknown. Our objective was to evaluate FA composition, identify changes in gene expression in the liver of male pigs fed diets enriched with different FA profiles, and identify impacted metabolic pathways and gene networks to enlighten the biological mechanisms' variation. Large White male pigs were randomly allocated to one of three diets with 18 pigs in each; all diets comprised a base of corn and soybean meal to which either 3% of soybean oil (SOY), 3% canola oil (CO), or 3% fish oil (FO) was added for a 98-day trial during the growing and finishing phases. RNA sequencing was performed on the liver samples of each animal by Illumina technology for differential gene expression analyses, using the R package DESeq2. The diets modified the FA profile, mainly in relation to polyunsaturated and saturated FAs. Comparing SOY vs. FO, 143 differentially expressed genes (DEGs) were identified as being associated with metabolism, metabolic and neurodegenerative disease pathways, inflammatory processes, and immune response networks. Comparing CO vs. SOY, 148 DEGs were identified, with pathways related to FA oxidation, regulation of lipid metabolism, and metabolic and neurodegenerative diseases. Our results help explain the behavior of genes with differential expression in metabolic pathways resulting from feeding different types of oils in pig diets.

Keywords: RNA-Seq; liver; metabolic disease; metabolic diseases; neurodegenerative diseases; pig; transcriptome.

PubMed Disclaimer

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Venn diagram of the comparison of 3.0% soybean oil vs. 3.0% fish oil (SOY vs. FO) and 3.0% canola oil vs. soybean oil (CO vs. SOY).
FIGURE 2
FIGURE 2
Pathway map representing the regulation of lipid metabolism_FXR-dependent negative feedback regulation of bile acid concentration using MetaCore software (p-value <0.10) based on the list of differentially expressed genes (FDR 10%) in the liver tissue of pigs fed with different oils in the diet (3.0% canola oil and 3.0% soybean oil). The blue thermometer indicates that the DEG is downregulated (log2-fold change −2.31 and −2.45) in the diet with 3.0% of canola oil (CO). Green arrows indicate positive interactions, and gray arrows indicate unspecified interactions.
FIGURE 3
FIGURE 3
Triacylglycerol biosynthesis in obesity and the diabetes mellitus type II pathway map by MetaCore software (p-value <0.10) from the list of differentially expressed genes (FDR 10%) in the liver tissue of pigs fed with different oils in the diet (3.0% canola oil and 3.0% soybean oil). The blue thermometer indicates that the DEG is downregulated (log2-fold change −4.72) in the diet with 3.0% of CO. Purple lines indicate increases in diseases. Green arrows indicate positive interactions, and gray arrows indicate unspecified interactions.
FIGURE 4
FIGURE 4
Top 10 enriched networks identified using MetaCore software applied to the list of differentially expressed genes (FDR 10%) in the liver tissue of male pigs fed with different oils (3.0% canola oil and 3.0% soybean oil).
FIGURE 5
FIGURE 5
Pathway maps from the list of differentially expressed genes (FDR 10%) in the liver of male pigs fed with different oil sources (3.0% soybean oil vs. 3.0% fish oil) detected using MetaCore software (p-value <0.10).
FIGURE 6
FIGURE 6
Role of the inflammasome in macrophages, adipocytes, and pancreatic beta cells in the type 2 diabetes pathway map based on MetaCore software (p-value <0.10) from the list of differentially expressed genes (FDR 10%) in the liver tissue of pigs fed with different oils in the diet (3.0% soybean oil and 3.0% fish oil). The blue thermometer indicates that the DEG is downregulated in the diet with 3.0% soybean oil (SOY). The large green arrows indicate the path to start. Green arrows indicate positive interactions, and gray arrows indicate unspecified interactions. Links in purple indicate emerging and enhanced (dotted) diseases.
See this image and copyright information in PMC

References

    1. Almeida V. V., Silva J. P. M., Schinckel A. P., Meira A. N., Moreira G. C. M., Gomes J. D., et al. (2021). Effects of increasing dietary oil inclusion from different sources on growth performance, carcass and meat quality traits, and fatty acid profile in genetically lean immunocastrated male pigs. Livest. Sci. 248, 104515. 10.1016/j.livsci.2021.104515 - DOI
    1. Aso Y., Okumura K. I., Takebayashi K., Wakabayashi S., Inukai T. (2003). Relationships of plasma interleukin-18 concentrations to hyperhomocysteinemia and carotid intimal-media wall thickness in patients with type 2 diabetes. Diabetes Care 26, 2622–2627. 10.2337/diacare.26.9.2622 - DOI - PubMed
    1. Baker E. J., Miles E. A., Burdge G. C., Yaqoob P., Calder P. C. (2016). Metabolism and functional effects of plant-derived omega-3 fatty acids in humans. Prog. Lipid Res. 64, 30–56. 10.1016/j.plipres.2016.07.002 - DOI - PubMed
    1. Benjamini Y., Hochberg Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57, 289–300. 10.1111/j.2517-6161.1995.tb02031.x - DOI
    1. Cesar A. S. M., Regitano L. C. A., Poleti M. D., Andrade S. C. S., Tizioto P. C., Oliveira P. S. N., et al. (2016). Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content. BMC Genomics 17, 961. 10.1186/s12864-016-3306-x - DOI - PMC - PubMed