Overexpression of PID1 reduces high density lipoprotein level and functionality in swine

Genome-Wide Association Analysis Reveals Novel Loci Related with Visual Score Traits in Nellore Cattle Raised in Pasture-Based Systems

Body conformation traits assessed based on visual scores are widely used in Zebu cattle breeding programs. The aim of this study was to identify genomic regions and biological pathways associated with body conformation (CONF), finishing precocity (PREC), and muscling (MUSC) in Nellore cattle. The measurements based on visual scores were collected in 20,807 animals raised in pasture-based systems in Brazil. In addition, 2775 animals were genotyped using a 35 K SNP chip, which contained 31,737 single nucleotide polymorphisms after quality control. Single-step GWAS was performed using the BLUPF90 software while candidate genes were identified based on the Ensembl Genes 69. PANTHER and REVIGO platforms were used to identify key biological pathways and STRING to create gene networks. Novel candidate genes were revealed associated with CONF, including ALDH9A1, RXRG, RAB2A, and CYP7A1, involved in lipid metabolism. The genes associated with PREC were ELOVL5, PID1, DNER, TRIP12, and PLCB4, which are related to the synthesis of long-chain fatty acids, lipid metabolism, and muscle differentiation. For MUSC, the most important genes associated with muscle development were SEMA6A, TIAM2, UNC5A, and UIMC1. The polymorphisms identified in this study can be incorporated in commercial genotyping panels to improve the accuracy of genomic evaluations for visual scores in beef cattle.

The Effect of BMI on Blood Lipids and Dyslipidemia in Lactating Women

Background: This study aimed to explore the correlation between body mass index (BMI) and dyslipidemia and the optimal cut-off point for BMI to distinguish the risk of dyslipidemia in lactating women. Methods: A total of 2295 lactating women subjects were included in this study, all within 2 years postpartum. All samples were from “China Children and Lactating Mothers Nutritional Health Surveillance (2016−2017)”. BMI, blood lipids, demographic information, lifestyle habits, and other serum indicators were obtained in this survey. Generalized linear model, logistic regression, restricted cubic spline (RCS) and ROC curve analysis were used to evaluate the relationship among BMI, blood lipids, and dyslipidemia. Results: BMI in lactating women was positively correlated with total cholesterol (TC), triglyceride (TG), low-density lipoprotein cholesterol (LDL-C), but negatively correlated with high-density lipoproteincholesterol (HDL-C) (p < 0.05). Higher BMI in lactating women was associated with higher ORs of dyslipidemia (hypercholesterolemia, hypertriglyceridemia, high-LDL-cholesterolemia, low HDL-cholesterolemia) (p < 0.05). These associations were stable across age groups, breastfeeding child age (months), parity, physical activity level, fasting plasma glucose (FPG), and hemoglobin. These factors did not interact with this relationship (p > 0.05). The optimal cut-off point for BMI was 24.85 kg/m2 determined by using ROC analysis, which can distinguish the risk of dyslipidemia. Conclusions: BMI was positively correlated with risk of dyslipidemia. Maintaining an ideal weight may prevent dyslipidemia in lactating women, and BMI is recommended to be controlled below 24.85 kg/m2.

RNA-seq reveals insights into molecular mechanisms of metabolic restoration via tryptophan supplementation in low birthweight piglet model

Low birth weight (LBW) is associated with metabolic disorders in early life. While dietary l-tryptophan (Trp) can ameliorate postprandial plasma triglycerides (TG) disposal in LBW piglets, the genetic and biological basis underlying Trp-caused alterations in lipid metabolism is poorly understood. In this study, we collected 24 liver samples from 1-mo-old LBW and normal birth weight (NBW) piglets supplemented with different concentrations of dietary Trp (NBW with 0% Trp, N0; LBW with 0% Trp, L0; LBW with 0.4% Trp, L4; LBW with 0.8% Trp, L8; N = 6 in each group.) and conducted systematic, transcriptome-wide analysis using RNA sequencing (RNA-seq). We identified 39 differentially expressed genes (DEG) between N0 and L0, and genes within “increased dose effect” clusters based on dose-series expression profile analysis, enriched in fatty acid response of gene ontology (GO) biological process (BP). We then identified RNA-binding proteins including SRSF1, DAZAP1, PUM2, PCBP3, IGF2BP2, and IGF2BP3 significantly (P < 0.05) enriched in alternative splicing events (ASE) in comparison with L0 as control. There were significant positive and negative relationships between candidate genes from co-expression networks (including PID1, ANKRD44, RUSC1, and CYP2J34) and postprandial plasma TG concentration. Further, we determined whether these candidate hub genes were also significantly associated with metabolic and cardiovascular traits in humans via human phenome-wide association study (Phe-WAS), and analysis of mammalian orthologs suggests a functional conservation between human and pig. Our work demonstrates that transcriptomic changes during dietary Trp supplementation in LBW piglets. We detected candidate genes and related BP that may play roles on lipid metabolism restoration. These findings will help to better understand the amino acid support in LBW metabolic complications.

Inclusion of endophenotypes in a standard GWAS facilitate a detailed mechanistic understanding of genetic elements that control blood lipid levels

Dyslipidemia is the primary cause of cardiovascular disease, which is a serious human health problem in large parts of the world. Therefore, it is important to understand the genetic and molecular mechanisms that regulate blood levels of cholesterol and other lipids. Discovery of genetic elements in the regulatory machinery is often based on genome wide associations studies (GWAS) focused on end-point phenotypes such as total cholesterol level or a disease diagnosis. In the present study, we add endophenotypes, such as serum levels of intermediate metabolites in the cholesterol synthesis pathways, to a GWAS analysis and use the pig as an animal model. We do this to increase statistical power and to facilitate biological interpretation of results. Although the study population was limited to ~ 300 individuals, we identify two genome-wide significant associations and ten suggestive associations. Furthermore, we identify 28 tentative associations to loci previously associated with blood lipids or dyslipidemia associated diseases. The associations with endophenotypes may inspire future studies that can dissect the biological mechanisms underlying these previously identified associations and add a new level of understanding to previously identified associations.