Co-expression of lncRNA correlates with traits of interest in an animal model for metabolic diseases in humans

Abstract

Nutrition plays an important role in the individual's health, as it directly influences the expression of specific genes responsible for important metabolic pathways (RAMOS-LOPEZ et al., 2017). According to Bouchard and Ordovas (2012), nutrigenomics has evolved to include the study of the effects of nutrients on gene expression and related molecular and biological events, incorporating important results from transcriptomics, proteomics and metabolomics. The importance of using pigs in nutrigenomics studies is their relevance in providing protein with high nutritional value and in the world economy through the production and consumption of their meat. Pork meat plays an important role in the human diet, consisting of protein sources with high biological value and essential fatty acids such as linoleic and linolenic acid (AG), providing nutrients that can provide people with safe, healthy and balanced diets (PARK et al., 2012; DUGAN et al., 2015; MOGHADASIAN and SHAHIDI, 2017). Previous studies by our study group showed that the addition of different levels of soybean oil to the diet of growing and finishing pigs is related both to the modification of liver gene expression profiles and to the involvement in the modulation of transcription factors (FANALLI et al., 2022; FANALI et al., 2023). In the liver, in a previous study carried out by the members of the group, the largest number of differentially expressed genes (GDE), 281 and signaling pathways related to neurodegenerative diseases were identified (FANALLI et al., 2022b). Among the recently identified regulatory RNAs are the lncRNA (long noncoding RNA) which are a heterogeneous class of ncRNA (noncoding RNA) that have more than 200 nucleotides, which are involved in several biological processes, including development, cell differentiation, immune responses, cell cycle and subcutaneous fat deposition, regulating gene expression. (HARROW et al., 2012; FATICA and BOZZONI, 2014; LIU et al., 2018). According to Zeng et al., 2018, lncRNA act on lipid metabolism by controlling adipogenesis, metabolism, transport of fatty acids (FA), cholesterol and phospholipids, and have the ability to act in the formation of high-density lipoproteins (HDL) and low density (LDL). Thus, the objective of this project is to carry out an lncRNA gene co-expression analysis and to correlate the co-expressed lncRNA groups with characteristics of economic and health interest following the methodology proposed by Zhang and Horvath (2005) and Langfelder and Horvath (2008), WGCNA (Weighted Correlation Network Analysis). This is a systems biology approach that allows identifying patterns of correlation or co-expression among thousands of genes expressed in a tissue at a given time based on large-scale gene expression data.