Effect of dietary soybean oil inclusion on liver-related transcription factors in a pig model for metabolic diseases.

Dietary fatty acids (FA) are components of the lipids, which contribute to membrane structure, energy input, and biological functions related to cellular signaling and transcriptome regulation. However, the consumers still associate dietary FA with fat deposition and increased occurrence of metabolic diseases such as obesity and atherosclerosis. Previous studies already demonstrated that some fatty acids are linked with inflammatory response, preventing metabolic diseases. To better understand the role of dietary FA on metabolic diseases, for the first time, a study to identify key transcription factors (TF) involved in lipid metabolism and inflammatory response by transcriptome analysis from liver samples of animal models was performed. The key TF were identified by functional enrichment analysis from the list of differentially expressed genes identified in liver samples between 35 pigs fed with 1.5% or 3.0% soybean oil. The functional enrichment analysis detected TF linked to lipid homeostasis and inflammatory response, such as RXRA, EGFR, and SREBP2 precursor. These findings demonstrated that key TF related to lipid metabolism could be modulated by dietary inclusion of soybean oil. It could contribute to nutrigenomics research field that aims to elucidate dietary interventions in animal and human health, as well as to drive food technology and science

Comparative transcriptome and gene co-expression networks associated with carcass traits of Nellore cattle

O objetivo deste trabalho foi estudar o transcriptoma do músculo Longissimus dorsi (LD) de bovinos da raça Nelore associado as características de área de olho de lombo (AOL) e espessura de gordura subcutânea (EGS), a fim de encontrar genes diferencialmente expressos (GDE), conjuntos de genes co-expressos, vias metabólicas e processos biológicos que regulam essas características. Foram utilizados dados de 385 bovinos Nelore castrados para obtenção das medidas fenotípicas de AOL e EGS, mensuradas entre a 12ª e 13ª costelas do músculo LD. Estes animais foram separados em dois grupos extremos, alto e baixo, contendo seis animais cada, baseados nos valores genômicos estimados (GEBV), para AOL e para EGS. Estes conjuntos de 12 animais foram submetidos à análise de expressão diferencial afim de encontrar GDE entre os grupos. Em seguida, a análise de enriquecimento funcional a partir da lista de GDE foi executada por meio do DAVID (Database for Annotation, Visualization and Integrated Discovery) e da combinação do BiNGO (Biological Networks Gene Ontology) e REVIGO (Reduce + Visualise Gene Ontology). Para AOL, foram identificados 101 GDE entre os grupos de alto e baixo GEBV. Desses, 72 genes apresentaram-se down-regulated e 29 up-regulated no grupo baixo. Para EGS, foram encontrados 18 GDE, dos quais treze apresentaram-se up-regulated e cinco down-regulated no grupo baixo. Dentre as vias metabólicas e processos biológicos encontrados para essas características, destacam-se a via de sinalização MAPK (bta04010) e a via da endocitose (bta04144) - AOL - e, os processos de biossíntese de andrógenos (GO:0006702) e via de sinalização canônica Wnt (GO:0060070) - EGS. Para encontrar conjuntos de genes co-expressos associados aos tratamentos (AOL e EGS), foi utilizado o pacote WGCNA (Weighted Correlation Network Analysis) do R, com dados de contagens de transcritos de 43 animais. Foram identificados 37 módulos, dentre eles, os módulos Azul, Verde-escuro e Salmon apresentaram correlação significativa de 0,3 com a EGS (P<0,10). Os genes destes módulos foram selecionados para análise de enriquecimento funcional quando seus valores de filiação ao módulo foram superiores a 0,7. O módulo azul apresentou o maior número de genes co-expressos, com 953 genes submetidos à análise de enriquecimento funcional. Foram encontradas seis vias metabólicas e 101 termos do Gene Ontology para este módulo, conforme análise do DAVID, além de 108 processos biológicos identificados pelo BiNGO/REVIGO. Os resultados do presente estudo enfatizam a complexidade da regulação gênica do músculo LD de bovinos Nelore associado às características de AOL e EGS. Estes resultados nos auxiliam a compreender melhor os diversos processos moleculares envolvidos na deposição muscular e de gordura de cobertura, características de carcaça economicamente importantes para a produção da carne bovina.The aim of this work was to study the Longissimus dorsi (LD) muscle transcriptome of Nellore cattle associated with ribeye area (REA) and backfat thickness (BFT) to find differentially expressed genes (DEG), coexpressed gene modules, metabolic pathways, and biological processes that regulate these traits. Data from 385 Nellore steers were used to obtain the phenotypic measures of REA and BFT, measured between the 12th and 13th ribs of the LD muscle. These animals were divided into two extreme groups, high and low, with six animals each, based on the estimated genomic breeding values (GEBV) for REA and for BFT. These sets of 12 animals were submitted to differentially expressed gene analysis to find DEG between the groups. Then, the functional enrichment analysis from the list of DEG was performed by DAVID (Database for Annotation, Visualization and Integrated Discovery) and the combination of BiNGO (Biological Networks Gene Ontology) and REVIGO (Reduce + Visualize Gene Ontology). For REA, 101 DEG were identified between the high and low GEBV groups. Of those, 72 genes were down-regulated and 29 up-regulated in the low group. For BFT, 18 DEG were found, of which thirteen were up-regulated and five were down-regulated in the low group. Among the metabolic pathways and biological processes found for these traits, the MAPK signaling pathway (bta04010) and the endocytosis pathway (bta04144) - for REA -, the androgen biosynthetic processes (GO: 0006702) and the canonical Wnt signaling pathway (GO: 0060070) - for EGS - can be highlighted. To find coexpressed gene modules associated with the traits (REA and BFT), we used the WGCNA (Weighted Correlation Network Analysis) package from R, with data from transcript counts of 43 animals. A total of 37 modules were founded. Among them, the Blue, Dark Green and Salmon modules had a significant correlation of 0.3 with BFT (P<0.10). The genes of these modules were selected for functional enrichment analysis when their module membership values were higher than 0.7. The blue module had the highest number of co-expressed genes, with 953 genes submitted to functional enrichment analysis. Six metabolic pathways and 101 Gene Oontology terms were founded for this module by DAVID analysis, in addition, 108 biological processes were identified by BiNGO/REVIGO. The results of the present study emphasize the complexity of gene regulation in the LD muscle of Nellore cattle associated with REA and BFT. These results can help us to better understand the different molecular processes involved in muscle and fat deposition, which are economically important carcass traits for beef production

Additional file 6: Figures S1 and S2. of Comparative muscle transcriptome associated with carcass traits of Nellore cattle

Plots of dispersion estimates of all ribeye area and backfat thickness genes. The black dots are the dispersion estimates of the empirical values of each gene; the red line represents the trend line; the blue dots represent the genes estimates regressed through the trend line used in the hypothesis test; and the blue circles above the “cloud” of points are genes which have high gene-wise dispersion estimates which are labelled as dispersion outliers, and will not be used in the hypothesis test. (PDF 110 kb

Comparative muscle transcriptome associated with carcass traits of Nellore cattle

Abstract Background Commercial cuts yield is an important trait for beef production, which affects the final value of the products, but its direct determination is a challenging procedure to be implemented in practice. The measurement of ribeye area (REA) and backfat thickness (BFT) can be used as indirect measures of meat yield. REA and BFT are important traits studied in beef cattle due to their strong implication in technological (carcass yield) and nutritional characteristics of meat products, like the degree of muscularity and total body fat. Thus, the aim of this work was to study the Longissimus dorsi muscle transcriptome of Nellore cattle, associated with REA and BFT, to find differentially expressed (DE) genes, metabolic pathways, and biological processes that may regulate these traits. Results By comparing the gene expression level between groups with extreme genomic estimated breeding values (GEBV), 101 DE genes for REA and 18 for BFT (false discovery rate, FDR 10%) were identified. Functional enrichment analysis for REA identified two KEGG pathways, MAPK (Mitogen-Activated Protein Kinase) signaling pathway and endocytosis pathway, and three biological processes, response to endoplasmic reticulum stress, cellular protein modification process, and macromolecule modification. The MAPK pathway is responsible for fundamental cellular processes, such as growth, differentiation, and hypertrophy. For BFT, 18 biological processes were found to be altered and grouped into 8 clusters of semantically similar terms. The DE genes identified in the biological processes for BFT were ACHE, SRD5A1, RSAD2 and RSPO3. RSAD2 has been previously shown to be associated with lipid droplet content and lipid biosynthesis. Conclusion In this study, we identified genes, metabolic pathways, and biological processes, involved in differentiation, proliferation, protein turnover, hypertrophy, as well as adipogenesis and lipid biosynthesis related to REA and BFT. These results enlighten some of the molecular processes involved in muscle and fat deposition, which are economically important carcass traits for beef production

Brain fatty acid and transcriptome profiles of pig fed diets with different levels of soybean oil

Background The high similarity in anatomical and neurophysiological processes between pigs and humans make pigs an excellent model for metabolic diseases and neurological disorders. Lipids are essential for brain structure and function. Polyunsaturated fatty acids (PUFA) have anti-inflammatory and positive effects against cognitive dysfunction in neurodegenerative diseases. Thus, our main goal was to evaluate the effect of different levels of dietary soybean oil on the lipid profile and brain tissue transcriptome in pigs. For this, thirty-six male pigs were used in a 98-day study. Treatments consisted of corn-soybean meal diets containing either 1.5% soybean oil (SOY1.5) or 3.0% soybean oil (SOY3.0). After slaughter, the brain samples were collected for total lipid content and fatty acid profile determination. Total mRNA extraction was performed for brain transcriptome sequencing. Results There were no differences for total lipid content and fatty acid profile between the two treatment groups. For differential expression analysis, a total of 34 differentially expressed genes (DEG, log2 fold change ≥ 1; ≤−1; FDR-corrected p-value < 0.05) between the SOY1.5 and SOY3.0 diets were identified by the DESeq2 statistical package. These DEG 25 were annotated, of which 11 were up-regulated and 14 were down-regulated for the SOY1.5 group compared to SOY3.0. The functional enrichment analysis performed by MetaCore with the 34 DEG (FDR < 0.05), identified four pathway maps (p-value < 0.05), which are related to the genes ALOX15B, CALB1 and CAST. The network calcium transport was also identified (p-value = 2.303e-2), with the CAST and CALB1 genes. Conclusion The results found in this study contribute to understanding the pathways and networks associated with processes involved intracellular calcium, lipid metabolism, and oxidative processes in brain tissue. Moreover, these results may aid in better understanding the modulating effects of soybean oil and its fatty acids (FA) composition on processes and diseases affecting brain tissue.This is a pre-print of the article da Silva, Bruna Pereira Martins, Simara Larissa Fanalli, Julia Dezen Gomes, Vivian Vezzoni de Almeida, Heidge Fukumasu, Felipe André Oliveira Freitas, Gabriel Costa Monteiro Moreira et al. "Brain fatty acid and transcriptome profiles of pig fed diets with different levels of soybean oil." Research Square (2022). DOI: 10.21203/rs.3.rs-1654172/v1 Copyright 2022 The Authors. Attribution 4.0 International (CC BY 4.0). Posted with permission

Effect of Dietary Soybean Oil Inclusion on Liver-Related Transcription Factors in a Pig Model for Metabolic Diseases

The objective of this study was to identify key transcription factors involved in lipid metabolism and immune response related to the differentially expressed genes (DEG) from the liver samples of 35 pig model for metabolic diseases fed diets containing either 1.5 or 3.0% soybean oil (SOY1.5 or SOY3.0). A total of 281 DEG between SOY1.5 and SOY3.0 diets (log2fold-change ≥ 1 or ≤ −1; FDR-corrected p-value &lt; 0.1) were identified, in which 129 were down-regulated and 152 were up-regulated in SOY1.5 group. The functional annotation analysis detected transcription factors linked to lipid homeostasis and immune response, such as RXRA, EGFR, and SREBP2 precursor. These findings demonstrated that key transcription factors related to lipid metabolism could be modulated by dietary inclusion of soybean oil. It could contribute to nutrigenomics research field that aims to elucidate dietary interventions in animal and human health, as well as to drive the food technology and science.This preprint is from Fanalli, S.L.; da Silva, B.P.M.; Gomes, J.D.; Ciconello, F.N.; de Almeida, V.V.; Freitas, F.A.O.; Moreira, G.C.M.; Silva-Vignato, B.; Afonso, J.; Reecy, J.; Koltes, J.; Koltes, D.; Regitano, L.C.D.A.; Baileiro, J.C.D.C.; Freitas, L.; Coutinho, L.L.; Fukumasu, H.; de Alencar, S.M.; Luchiari Filho, A.; Cesar, A.S.M. Effect of Dietary Soybean Oil Inclusion on Liver-Related Transcription Factors in a Pig Model for Metabolic Diseases. Preprints 2022, 2022020149 (doi: 10.20944/preprints202202.0149.v1). This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

Differential Gene Expression Associated with Soybean Oil Level in the Diet of Pigs

The aim of this study was to identify the differentially expressed genes (DEG) from the skeletal muscle and liver samples of animal models for metabolic diseases in humans. To perform the study, the fatty acid (FA) profile and RNA sequencing (RNA-Seq) data of 35 samples of liver tissue (SOY1.5, n = 17 and SOY3.0, n = 18) and 36 samples of skeletal muscle (SOY1.5, n = 18 and SOY3.0, n = 18) of Large White pigs were analyzed. The FA profile of the tissues was modified by the diet, mainly those related to monounsaturated (MUFA) and polyunsaturated (PUFA) FA. The skeletal muscle transcriptome analysis revealed 45 DEG (FDR 10%), and the functional enrichment analysis identified network maps related to inflammation, immune processes, and pathways associated with oxidative stress, type 2 diabetes, and metabolic dysfunction. For the liver tissue, the transcriptome profile analysis revealed 281 DEG, which participate in network maps related to neurodegenerative diseases. With this nutrigenomics study, we verified that different levels of soybean oil in the pig diet, an animal model for metabolic diseases in humans, affected the transcriptome profile of skeletal muscle and liver tissue. These findings may help to better understand the biological mechanisms that can be modulated by the diet

Transcriptome profile of skeletal muscle using different sources of dietary fatty acids in male pigs

Background Pork is of great importance in world trade and represents the largest source of fatty acids in the human diet. Lipid sources such as soybean oil (SOY), canola (CO), and fish oil (FO) are used in pig diets and influence blood parameters and the ratio of deposited fatty acids. Scientific studies that improve our nutrigenomic knowledge about pig and human health through the consumption of pork are of great importance. In this study, the main objective was to evaluate changes in gene expression in porcine skeletal muscle tissue resulting from the dietary oil sources and to identify metabolic pathways and biological process networks through RNA-Seq. Results The addition of FO in the diet of pigs led to intramuscular lipid with a higher FA profile composition of C20:5 n-3, C22:6 n-3, and SFA (C16:0 and C18:0). Blood parameters for the FO group showed lower cholesterol and HDL content compared with CO and SOY groups. Skeletal muscle transcriptome analyses revealed 65 differentially expressed genes (DEG, FDR 10%) between CO vs SOY, and 531 DEG for SOY vs FO comparison, and 32 DEG for CO vs FO. The enrichment analysis of the DEG lists revealed lipid metabolism, metabolic diseases, and inflammation processes networks, such as "regulation of lipid metabolism: RXR-dependent regulation of lipid metabolism via PPAR, RAR and VDR", “transport HDL-mediated reverse cholesterol transport”, and "TNF- α , IL-1 β induce dyslipidemia and inflammation in obesity and type 2 diabetes in adipocytes". Conclusion The genes identified in this study provided relevant information on biological processes and lipid metabolism pathways. The enrichment of the basal diet with oil containing different FA profiles influenced fatty acid composition of intramuscular fat, blood parameters, and the gene differential expression in metabolic pathways and processes network in skeletal muscle of pigs. The results provide mechanisms to help us understand the behavior of genes according to fatty acids.This preprint is available from Research Square at doi:10.21203/rs.3.rs-1795454/v1.This work is licensed under a Creative Commons Attribution 4.0 International License