Demystifying molecular biology and functional foods

Resumo do Congresso de Graduação da USP 2021

Different oil sources impacting brain lipid and transcriptome profiles of pigs

Lipids are fundamental to the structure and function of the brain, and their fatty acids (FA) composition is rich in polyunsaturated fatty acids (PUFA), which have protective effects and modulate gene transcription. For nutrigenomics studies, pigs (Sus scrofa) have been widely used as a biomedical model. Thus, the aimed to investigate whether different dietary oil sources modify the pig brain's lipid and transcriptomic profile. A 98-day study was performed using fifty-four male pigs. Treatments consisted of corn-soybean meal diets containing 3 % of soybean oil (SOY), canola oil (CO), or fish oil (FO). Total mRNA was extracted for sequencing. As a result, feeding diets with different oil sources affected the percentage of some FA. Palmitic acid showed a greater concentration in diets containing SOY with 27.037 %. Oleic acid and eicosenoic acid, showed a greater concentration in diets containing SOY, with 30.968 % and 2.096 %, respectively; and, total PUFA showed a better concentration in diets containing SOY and FO, with 11.685 % and 12.150 %, respectively. After quality control, considering the total reads obtained for the three groups, 94.87% were mapped against the reference genome SScrofa11.1. A comparison of gene expression between the groups of pigs was carried out by using the DESeq2 statistical package (R/Bioconductor). From SOY vs CO comparison, five differentially expressed genes (DEG, FDR < 0.05) were identified, from SOY vs FO forty-four DEG were verified, and from CO vs FO thirty-nine DEG were found. The functional enrichment analysis resulted in pathway maps (P < 0.05) related to apoptosis and cell proliferation, obesity and type 2 diabetes, neurophysiological process, and inflammation. The networks were associated with signal transduction, calcium transport, and oxidative stress. Overall, the results showed that diets with different oil sources could affect some brain tissue parameters and may help guide future research on the availability of dietary FA in the brain.This article is published as da Silva, Bruna Pereira Martins, Simara Larissa Fanalli, Julia Dezen Gomes, Vivian Vezzoni de Almeida, Heidge Fukumasu, Gabriel Costa Monteiro Moreira, Bárbara Silva-Vignato et al. "Different oil sources impacting brain lipid and transcriptome profiles of pigs." Livestock Science 284 (2024): 105490. doi:10.1016/j.livsci.2024.105490. © 2024 The Author(s). This is an open access article under the CC BY-NC license (http://creativecommons.org/licenses/by-nc/4.0/)

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

Efeito da adição de diferentes fontes de ácidos graxos na dieta de suínos sobre o perfil do transcriptoma de diferentes tecidos

The Sus Scrofa species is one of the most important for the production of meat and other animal products worldwide and is an animal model for metabolic diseases in humans. Furthermore, pork is one of the main sources of fatty acids (FA) in the human diet. The FA consumption is associated with fat deposition and increased occurrence of metabolic diseases. On the other hand, some studies diverge on the role of FAs involved in cellular inflammatory responses in metabolic diseases. The aim of this study was to identify differentially expressed genes (GDE) and transcription factors from muscle and liver samples from immunocastrated male pigs fed a diet added from different sources and levels of FA. Dietary treatments consisted of corn-soybean meal growing-finishing diets supplemented with 1.5% soybean oil (SOY1.5, common level used in commercial pig production) or 3% soybean oil (SOY3.0) or 3% canola oil (CO) or 3% fish oil (FO) for an experimental period of 98 days during the growing and finishing phases (18 pigs/treatment). The analysis of the parameters of the blood was performed, as well as the profile of AG deposited in the tissues. The DEG (FDR 10%) was identified in 72 samples of skeletal muscle and liver using the DESeq2 R., followed by data quality analysis. From the transcriptome analysis of skeletal muscle and liver samples, the functional enrichment analysis (FDR &lt;0.10) by MetaCore revealed maps of signaling pathways associated with metabolic processes, oxidative stress, metabolic and neurodegenerative diseases, as well as gene networks related to immune response and biological processes. The enrichment of the basal diet with oil sources containing different FA profiles influenced the composition of the deposited profile, the blood parameters, and the gene expression in metabolic pathways and network processes in the skeletal muscle tissue and liver of animals during the growth and termination. When the comparison was related to the addition of soybean oil and fish oil, the highest amount of total DEG was identified. In addition, transcription factors related to lipid metabolism and immune response were identified when using 1.5% or 3% soybean oil. It could contribute to the nutrigenomics research field that aims to elucidate dietary interventions in animal and human health, as well as to drive food technology and Science.A espécie Sus Scrofa é uma das mais importantes para a produção de carne e outros produtos de origem animal em todo o mundo e são modelo animal para doenças metabólicas em humanos. Além disso, a carne suína é uma das principais fontes de ácidos graxos (AG) na dieta humana. O consumo de AG está associado à deposição de gordura e aumento da ocorrência de doenças metabólicas. Por outro lado, existem estudos que divergem sobre o papel dos AG envolvidos nas respostas inflamatórias celulares em doenças metabólicas. O objetivo deste estudo foi identificar os genes diferencialmente expressos (GDE) e os fatores de transcrição de amostras de músculo e fígado de suínos machos imunocastrados alimentados com dieta adicionada de diferentes fontes e níveis de AG. Os tratamentos dietéticos consistiram em dieta basal de milho e farelo de soja suplementadas com 1,5% de óleo de soja (SOY1,5, nível comum usado na produção comercial de suínos) ou 3% de óleo de soja (SOY3,0), ou 3% de óleo de canola (CO) ou 3% de óleo de peixe (FO) por um período experimental de 98 dias durante as fases de crescimento e terminação (18 animais/tratamento). Foi realizada a análise dos parâmetros bioquímicos do sangue, assim como o perfil de AG depositados nos tecidos. Os GDE (FDR 10%) foram identificados em 72 amostras de músculo esquelético e fígado através do pacote DESeq2 R, seguido da análise de qualidade dos dados. A partir da análise do transcriptoma de amostras do músculo esquelético e fígado, a análise de enriquecimento funcional (FDR&lt;0,10) pelo MetaCore resultou em mapas de vias de sinalização associadas a processos metabólicos, estresse oxidativo doenças metabólicas e neurodegenerativas, assim como redes gênicas relacionadas à resposta imune e processos biológicos. O enriquecimento da dieta basal com fontes de óleo contendo diferentes perfis de AG influenciou a composição do perfil depositado na gordura intramuscular (Longissimus lomborum) e fígado, os parâmetros sanguíneos e a expressão gênica em vias metabólicas e processos de redes no tecido muscular esquelético e fígado dos animais durante as fases de crescimento e terminação. Quando a comparação foi relacionada à adição de óleo de soja e óleo de peixe a maior quantidade de GDE total foi identificada. Além disso, fatores de transcrição foram relacionados ao metabolismo lipídico e resposta imune quando utilizado óleo de soja 1.5% ou 3%. Em suma, esses resultados contribuem para o campo de pesquisa da nutrigenômica que visa elucidar a influência da dieta na saúde animal e humana e impulsionar a tecnologia e a ciência dos alimentos

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 model for metabolic diseases in human. 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 process, and pathways associated with the 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.This article is published as Fanalli, Simara Larissa, Bruna Pereira Martins Da Silva, Julia Dezen Gomes, Vivian Vezzoni De Almeida, Felipe André Oliveira Freitas, Gabriel Costa Monteiro Moreira, Bárbara Silva-Vignato et al. "Differential Gene Expression Associated with Soybean Oil Level in the Diet of Pigs." Preprints (2022). DOI: 10.20944/preprints202205.0081.v1. Copyright 2022 by the author(s). Attribution 4.0 International (CC BY 4.0). Posted with permission

Effects of Dietary Fatty Acids on Gene Expression and Biological Processes in Different Tissues of Pigs: A Review

Studies on the influence of dietary components and their effects are fundamental for nutrigenomics, or the study of how nutrients can be cellular sensors, how they affect biological processes and gene expression in different tissues. Lipids are an important source of fatty acids (FA) and energy and are fundamental to biological processes and influence the regulation of transcription. Pigs are excellent model to study nutrigenomics, particularly lipid metabolism because the deposition and composition of FA in their tissues reflect the composition of FA in their diet. Recent studies show that FA supplementation is important in production systems, such as growing and finishing pigs, as it can improve the energy value of the feed, help reduce costs, improve animal welfare, and influence the nutritional value of the meat. Studies show that oleic (OA), linoleic (LA), docosahexaenoic (DHA), and eicosapentaenoic (EPA) acids are associated with the regulation of transcription in tissues such as muscle, liver, adipose tissue, and brain. Other studies indicate that EPA and DHA are associated with changes in specific signaling pathways, altering gene expression and biophysical properties of membranes. This review, therefore, focuses on the current knowledge of the effects of dietary FA on production traits and gene expression.This preprint is made available through Preprints, doi:10.20944/preprints202111.0279.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

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

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

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

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