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E-GEOD-72123 - Effect of a diet enriched with omega-6 and omega-3 fatty acids on the pig liver transcriptome

Status
Released on 15 March 2016, last updated on 19 March 2016
Organism
Sus scrofa
Samples (2)
Protocols (2)
Description
The optimal ratio of omega-6 to omega-3 polyunsaturated fatty acids (PUFAs) is important for keeping homeostasis of biological processes and metabolism, yet the underlying biological mechanism is poorly understood. The objective of this study was to identify changes in the pig liver transcriptome induced by a diet enriched with omega-6 and omega-3 fatty acids, and to characterize the biological mechanisms related to PUFA metabolism. Polish Landrace pigs (n =12) were fed diet enriched with linoleic acid (LA, omega-6) and alpha-linolenic acid (ALA, omega-3 family) or standard diet as a control. The fatty acids profiling was assayed in order to verify how feeding influenced the fatty acids content in liver, and subsequently next-generation sequencing (NGS) was used to identify differentially expressed genes (DEG) between transcriptomes between dietary groups. The biological mechanisms and pathway interaction networks were identified by analysis in DAVID and Cytoscape tools. Fatty acids profile analysis indicated a higher contribution of PUFAs in liver for LA and ALA-enriched diet group, particularly for the omega-3 fatty acids family, but not omega-6. Next-generation sequencing identified 3,565 DEG, 1,484 of which were induced and 2,081 were suppressed by PUFA supplemenation. Low ratio of omega-6/-3 fatty acids resulted in modulation of fatty acids metabolism pathways and over-representation of genes involved in membrane composition, signal transduction and immune response pathways. In conclusion, a diet enriched with omega-6 and omega-3 fatty acids altered the transcriptomic profile of the pig liver and affected a set of genes involved in metabolic pathways important to animal health status. Hepatic mRNA profiles of Polish Landrace pig breed fed two different diets, were generated by deep sequencing, using Illumina MiSeq. Experimental diet was enriched with polyunsaturated fatty acids (omega-6 and omega-3), while standard diet remain as a cotrol. 2 pooled samples each containing RNA extracts from 6 individuals livers were analyzed.
Experiment type
RNA-seq of coding RNA 
Contacts
Agnieszka Szostak <a.szostak@ighz.pl>, Chandra Shekhar Pareek, Edyta Juszczuk-Kubiak, Ewa Poławska, Jarosław O Horbańczuk, Jenelle R Dunkelberger, Magdalena Ogłuszka, Marinus F te Pas, Mariusz Pierzchała, Paweł Urbański, Tadeusz Blicharski
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-72123.idf.txt
Sample and data relationshipE-GEOD-72123.sdrf.txt
Processed data (1)E-GEOD-72123.processed.1.zip
Links