Expression levels of brown/beige adipocyte-related genes in fat depots of vitamin A-restricted fattening cattle1

Association of ARRDC3 and NFIA variants with bovine congestive heart failure in feedlot cattle

Background

Bovine congestive heart failure (BCHF) has become increasingly prevalent among feedlot cattle in the Western Great Plains of North America with up to 7% mortality in affected herds. BCHF is an untreatable complex condition involving pulmonary hypertension that culminates in right ventricular failure and death. Genes associated with BCHF in feedlot cattle have not been previously identified. Our aim was to search for genomic regions associated with this disease.

Methods

A retrospective, matched case-control design with 102 clinical BCHF cases and their unaffected pen mates was used in a genome-wide association study. Paired nominal data from approximately 560,000 filtered single nucleotide polymorphisms (SNPs) were analyzed with McNemar's test.

Results

Two independent genomic regions were identified as having the most significant association with BCHF: the arrestin domain-containing protein 3 gene ( ARRDC3), and the nuclear factor IA gene ( NFIA, mid- p-values, 1x10 -8 and 2x10 -7, respectively). Animals with two copies of risk alleles at either gene were approximately eight-fold more likely to have BCHF than their matched pen mates with either one or zero risk alleles at both genes (CI 95 = 3-17). Further, animals with two copies of risk alleles at both genes were 28-fold more likely to have BCHF than all others ( p-value = 1×10 -7, CI 95 = 4-206). A missense variant in ARRDC3 (C182Y) represents a potential functional variant since the C182 codon is conserved among all other jawed vertebrate species observed. A two-SNP test with markers in both genes showed 29% of 273 BCHF cases had homozygous risk genotypes in both genes, compared to 2.5% in 198 similar unaffected feedlot cattle. This and other DNA tests may be useful for identifying feedlot animals with the highest risk for BCHF in the environments described here.

Conclusions

Although pathogenic roles for variants in the ARRDC3 and NFIA genes are unknown, their discovery facilitates classifying animals by genetic risk and allows cattle producers to make informed decisions for selective breeding and animal health management.

Insights into the influence of diet and genetics on feed efficiency and meat production in sheep

Feed costs and carcass yields affect the profitability and sustainability of sheep production. Therefore, it is crucial to select animals with a higher feed efficiency and high-quality meat production. This study focuses on the impact of dietary and genetic factors on production traits such as feed efficiency, carcass quality, and meat quality. Diets promote optimal sheep growth and development and provide sufficient protein can lead to higher-quality meat. However, establishing an optimized production system requires careful consideration and balance of dietary parameters. This includes ensuring adequate protein intake and feeding diets with higher intestinal absorption rates to enhance nutrient absorption in the gut. The study identifies specific genes, such as Callipyge, Calpastatin, and Myostatin, and the presence of causal mutations in these genes, as factors influencing animal growth rates, feed efficiency, and meat fatty acid profiles. Additionally, variants of other reported genes, including PIGY, UCP1, MEF2B, TNNC2, FABP4, SCD, FASN, ADCY8, ME1, CA1, GLIS1, IL1RAPL1, SOX5, SOX6, and IGF1, show potential as markers for sheep selection. A meta-analysis of reported heritability estimates reveals that residual feed intake (0.27 ± 0.07), hot carcass weight (0.26 ± 0.05), dressing percentage (0.23 ± 0.05), and intramuscular fat content (0.45 ± 0.04) are moderately to highly heritable traits. This suggests that these traits are less influenced by environmental factors and could be improved through genetic selection. Additionally, positive genetic correlations exist between body weight and hot carcass weight (0.91 ± 0.06), dressing percentage (0.35 ± 0.15), and shear force (0.27 ± 0.24), indicating that selecting for higher body weight could lead to favorable changes in carcass quality, and meat quality.

LSD1 for the Targeted Regulation of Adipose Tissue

White and thermal (brown and beige) adipose tissue energy storage and oxidative regulation pathways play a central role in maintaining the energy balance throughout the body, and the dysregulation of these pathways is closely related to glucose and lipid metabolism disorders and adipose tissue dysfunction, including obesity, chronic inflammation, insulin resistance, mitochondrial dysfunction, and fibrosis. Recent epigenetic studies have identified the novel regulatory element LSD1, which controls the above parameters, and have provided new mechanistic possibilities for re-encoding the fate and function of adipocytes. In this review, we outline the current advances in adipocyte metabolism in physiology and disease and discuss possible strategies for LSD1 to alter the phenotype of adipose tissue and thus influence energy utilization to improve metabolic health.

Multi-omic data integration for the study of production, carcass, and meat quality traits in Nellore cattle

Data integration using hierarchical analysis based on the central dogma or common pathway enrichment analysis may not reveal non-obvious relationships among omic data. Here, we applied factor analysis (FA) and Bayesian network (BN) modeling to integrate different omic data and complex traits by latent variables (production, carcass, and meat quality traits). A total of 14 latent variables were identified: five for phenotype, three for miRNA, four for protein, and two for mRNA data. Pearson correlation coefficients showed negative correlations between latent variables miRNA 1 (mirna1) and miRNA 2 (mirna2) (−0.47), ribeye area (REA) and protein 4 (prot4) (−0.33), REA and protein 2 (prot2) (−0.3), carcass and prot4 (−0.31), carcass and prot2 (−0.28), and backfat thickness (BFT) and miRNA 3 (mirna3) (−0.25). Positive correlations were observed among the four protein factors (0.45–0.83): between meat quality and fat content (0.71), fat content and carcass (0.74), fat content and REA (0.76), and REA and carcass (0.99). BN presented arcs from the carcass, meat quality, prot2, and prot4 latent variables to REA; from meat quality, REA, mirna2, and gene expression mRNA1 to fat content; from protein 1 (prot1) and mirna2 to protein 5 (prot5); and from prot5 and carcass to prot2. The relations of protein latent variables suggest new hypotheses about the impact of these proteins on REA. The network also showed relationships among miRNAs and nebulin proteins. REA seems to be the central node in the network, influencing carcass, prot2, prot4, mRNA1, and meat quality, suggesting that REA is a good indicator of meat quality. The connection among miRNA latent variables, BFT, and fat content relates to the influence of miRNAs on lipid metabolism. The relationship between mirna1 and prot5 composed of isoforms of nebulin needs further investigation. The FA identified latent variables, decreasing the dimensionality and complexity of the data. The BN was capable of generating interrelationships among latent variables from different types of data, allowing the integration of omics and complex traits and identifying conditional independencies. Our framework based on FA and BN is capable of generating new hypotheses for molecular research, by integrating different types of data and exploring non-obvious relationships.

Relationships between the expression of adipose genes and profiles of hospitalized dogs

Obesity is one of the risk factors for the onset of various metabolic diseases in dogs. Energy expenditure in brown/beige adipocytes, which is partially regulated by the bone morphogenetic protein (BMP) pathway, is a key factor determining systemic energy balance. Here, we examined gene expression in the fat depots of 129 hospitalized dogs, and the relationship between the relative levels of gene expression and profiles of dogs. We evaluated the expression levels of 23 genes such as regulatory genes of adipocyte differentiation and function, adipokines, genes related to brown adipogenesis and uncoupling protein (Ucp), and genes involved in BMP signaling. A reliable equation of multiple regression was not obtained to explain the body condition score (BCS), which is an index of adiposity. Positive relationships were detected between the expression levels of many genes, except for Ucp1 or Ucp3. BCS was found to increase with age. BCS was negatively correlated to the expression levels of Pparγ and Fasn, and positively correlated to Leptin and Opn3 expression. Aging decreased the expression levels of genes related to adipocyte differentiation and function (Pparγ, Fabp4, Fasn, Hsl, and Insr) and Adipoq. In addition, age was negatively correlated with the expression of genes involved in brown adipogenesis and BMP signaling components (Prdm16, Bmp4, Alk3, Actr2a, and Actr2b). In contrast, the expression levels of Leptin and Ucp2 were found to increase with age. The present study clarifies BCS- and age-related gene expressions in the adipose tissue, which potentially contribute to elucidating the etiology of canine obesity.

Integrated Analysis of Transcriptome, microRNAs, and Chromatin Accessibility Revealed Potential Early B-Cell Factor1-Regulated Transcriptional Networks during the Early Development of Fetal Brown Adipose Tissues in Rabbits

In domestic mammals, cold stress decreases the survival rate of newborns and increases the cost of management. Brown adipose tissue (BAT) is the main thermogenic organ for cubs, and well-developed fetal BAT (FBAT) is beneficial for newborns to maintain core temperatures during the first several days of life. However, our knowledge of the epigenetic mechanisms during the early development of FBAT remains largely unknown. Rabbits (Oryctolagus cuniculus) are economically important domestic animals. In this study, a histological analysis shows that the tissue content, thermogenic capacity, and lipid content of FBAT dramatically increases from gestational day 21 (G21) to gestational day 24 (G24) in rabbits. RNA-seq, microRNA-seq (miRNA-seq), and the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) show that many genes, miRNAs, and chromatin-accessible regions (referred to as peaks) were identified as significantly changed from G21 to G24, respectively. The upregulated genes from G21 to G24 were significantly enriched in the mitochondrial metabolism and thermogenesis-related signal pathways. The integrated analysis of transcriptome and chromatin accessibility reveals that the peaks in the promoters have a more regulatory effect than peaks in other genomic elements on the expression of their nearby genes in FBATs. The upregulated genes that are associated with increased chromatin accessibility in the promoter regions are involved in the energy metabolism-related signaling pathways. The genes that have a greater tendency to be regulated by miRNAs than the chromatin accessibility in gene promoters are involved in the apelin, insulin, and endocytosis signaling pathways. Furthermore, genome-wide transcription factor (TF) footprinting analysis identifies early B-cell factor1 (EBF1) as playing a key role during early FBAT development. The carbon metabolism, citrate cycle, and PPAR signaling pathways are significantly enriched by the predicted EBF1-regulated cascade TF-network. In conclusion, our work provides a framework for understanding epigenetics regulatory mechanisms underlying the early development of FBAT and identifies potential TF involved in the early development of FBAT in rabbits.

Neonatal infrared thermography images in the hypothermic ruminant model: Anatomical-morphological-physiological aspects and mechanisms for thermoregulation

Hypothermia is one factor associated with mortality in newborn ruminants due to the drastic temperature change upon exposure to the extrauterine environment in the first hours after birth. Ruminants are precocial whose mechanisms for generating heat or preventing heat loss involve genetic characteristics, the degree of neurodevelopment at birth and environmental aspects. These elements combine to form a more efficient mechanism than those found in altricial species. Although the degree of neurodevelopment is an important advantage for these species, their greater mobility helps them to search for the udder and consume colostrum after birth. However, anatomical differences such as the distribution of adipose tissue or the presence of type II muscle fibers could lead to the understanding that these species use their energy resources more efficiently for heat production. The introduction of unconventional ruminant species, such as the water buffalo, has led to rethinking other characteristics like the skin thickness or the coat type that could intervene in the thermoregulation capacity of the newborn. Implementing tools to analyze species-specific characteristics that help prevent a critical decline in temperature is deemed a fundamental strategy for avoiding the adverse effects of a compromised thermoregulatory function. Although thermography is a non-invasive method to assess superficial temperature in several non-human animal species, in newborn ruminants there is limited information about its application, making it necessary to discuss the usefulness of this tool. This review aims to analyze the effects of hypothermia in newborn ruminants, their thermoregulation mechanisms that compensate for this condition, and the application of infrared thermography (IRT) to identify cases with hypothermia.

Adipose Tissue Aging and Metabolic Disorder, and the Impact of Nutritional Interventions

Adipose tissue is the largest and most active endocrine organ, involved in regulating energy balance, glucose and lipid homeostasis and immune function. Adipose tissue aging processes are associated with brown adipose tissue whitening, white adipose tissue redistribution and ectopic deposition, resulting in an increase in age-related inflammatory factors, which then trigger a variety of metabolic syndromes, including diabetes and hyperlipidemia. Metabolic syndrome, in turn, is associated with increased inflammatory factors, all-cause mortality and cognitive impairment. There is a growing interest in the role of nutritional interventions in adipose tissue aging. Nowadays, research has confirmed that nutritional interventions, involving caloric restriction and the use of vitamins, resveratrol and other active substances, are effective in managing adipose tissue aging’s adverse effects, such as obesity. In this review we summarized age-related physiological characteristics of adipose tissue, and focused on what nutritional interventions can do in improving the retrogradation and how they do this.

Regulatory expression of uncoupling protein 1 and its related genes by endogenous activity of the transforming growth factor-β family in bovine myogenic cells

Uncoupling protein 1 (UCP1) is responsible for non-shivering thermogenesis, with restricted expression in brown/beige adipocytes in humans and rodents. We have previously shown an unexpected expression of UCP1 in bovine skeletal muscles. This study evaluated factors affecting Ucp1 gene expression in cultured bovine myogenic cells. Myosatellite cells, which were isolated from the bovine musculus longissimus cervicis, were induced to differentiate into myotubes in the presence of 2% horse serum. Previous studies using murine brown/beige adipocytes revealed that Ucp1 expression levels are directly increased by forskolin and all-trans retinoic acid (RA). The transforming growth factor-β (TGF-β)/activin pathway negatively regulated Ucp1 expression, whereas activation of the bone morphogenetic protein (BMP) pathway indirectly increases Ucp1 expression through the stimulation of brown/beige adipogenesis. Neither forskolin nor RA significantly affected Ucp1 mRNA levels in bovine myogenic cells. A-83-01, an inhibitor of the TGF-β/activin pathway, stimulated myogenesis in these cells. A-83-01 significantly increased the expression of some brown fat signature genes such as Pgc-1α, Cox7a1, and Dio2, with a quantitative but not significant increase in the expression of Ucp1. Treatment with LDN-193189, an inhibitor of the BMP pathway, did not affect the differentiation of bovine myosatellite cells. Rather, LDN-193189 increased Ucp1 mRNA levels without modulating the levels of other brown/beige adipocyte-related genes. The current results indicate that the regulation of Ucp1 expression in bovine myogenic cells is distinct from that in murine brown/beige adipocytes, which has been more intensely characterized. SIGNIFICANCE OF THE STUDY: We previously reported unexpected expression of Ucp1 in bovine muscle tissues; Ucp1 expression has been known to be detected predominantly in brown/beige adipocytes. This study examined regulatory expression of bovine Ucp1 in myogenic cells. Consistent with the changes in expression levels of brown/beige adipocyte-selective genes, Ucp1 expression tended to be increased by inhibition of endogenous TGF-β activity. In contrast, inhibition of endogenous BMP significantly increased Ucp1 expression without affecting brown/beige adipocyte-selective gene expression. The current results indicate that regulatory expression of Ucp1 in bovine myogenic cells is distinct from that in murine brown/beige adipocytes that is more intensely characterized.

Carotenoids and carotenoid conversion products in adipose tissue biology and obesity: Pre-clinical and human studies

Antiobesity activities of carotenoids and carotenoid conversion products (CCPs) have been demonstrated in pre-clinical studies, and mechanisms behind have begun to be unveiled, thus suggesting these compounds may help obesity prevention and management. The antiobesity action of carotenoids and CCPs can be traced to effects in multiple tissues, notably the adipose tissues. Key aspects of the biology of adipose tissues appear to be affected by carotenoid and CCPs, including adipogenesis, metabolic capacities for energy storage, release and inefficient oxidation, secretory function, and modulation of oxidative stress and inflammatory pathways. Here, we review the connections of carotenoids and CCPs with adipose tissue biology and obesity as revealed by cell and animal intervention studies, studies addressing the role of endogenous retinoid metabolism, and human epidemiological and intervention studies. We also consider human genetic variability influencing carotenoid and vitamin A metabolism, particularly in adipose tissues, as a potentially relevant aspect towards personalization of dietary recommendations to prevent or manage obesity and optimize metabolic health. This article is part of a Special Issue entitled Carotenoids recent advances in cell and molecular biology edited by Johannes von Lintig and Loredana Quadro.

Novel lncRNA lncFAM200B: Molecular Characteristics and Effects of Genetic Variants on Promoter Activity and Cattle Body Measurement Traits

Skeletal muscle is one of the three major muscle types in an organism and has key roles in the motor system, metabolism, and homeostasis. RNA-Seq analysis showed that novel lncRNA, lncFAM200B, was differentially expressed in embryonic, neonatal, and adult cattle skeletal muscles. The main aim of this study was to investigate the molecular and expression characteristics of lncFAM200B along with its crucial genetic variations. Our results showed that bovine lncFAM200B was a 472 nucleotide (nt) non-coding RNA containing two exons. The transcription factor binding site prediction analysis found that lncFAM200B promoter region was enriched with SP1 transcription factor, which promotes the binding of myogenic regulatory factor MyoD and DNA sequence. The mRNA expression analysis showed that lncFAM200B was differentially expressed in embryonic, neonatal, adult bovine muscle tissues, and the lncFAM200B expression trend positively correlated with that of MyoG and Myf5 in myoblast proliferation and differential stages. To identify the promoter active region of lncFAM200B, we constructed promoter luciferase reporter gene vector pGL3-Basic plasmids containing lncFAM200B promoter sequences and transfected them into 293T, C2C12, and 3T3-L1 cells. Our results suggested that lncFAM200B promoter active region was from −403 to −139 (264 nt) of its transcription start site, covering 6 SP1 potential binding sites. Furthermore, we found a novel C-T variation, named as SNP2 (ERZ990081 in European Variation Archive) in the promoter active region, which was linked to the nearby SNP1 (rs456951291 in Ensembl database). The genotypes of SNP1 and combined genotypes of SNP1 and SNP2 were significantly associated with Jinnan cattle hip height. The luciferase activity analysis found that the SNP1-SNP2 haplotype CC had the highest luciferase activity, which was consistent with the association analysis result that the combined genotype CC-CC carriers had the highest hip height in Jinnan cattle. In conclusion, our data showed that lncFAM200B is a positive regulator of muscle development and that SNP1 and SNP2 could be used as genetic markers for marker-assisted selection (MAS) breeding of beef cattle.

Relationships between expression levels of genes related to adipogenesis and adipocyte function in dogs

There are three kinds of adipocytes; white adipocytes accumulate excess energy as fat, whereas brown/beige adipocytes dissipate energy through expression of uncoupling protein 1 (UCP1). Obesity, a feature of excess accumulation of white adipocytes in a body, is one of the risk factors for onset of various diseases in dogs. As the first step to explore adipose genes related to dog obesity, we examined relationships among mRNA levels of putative molecules related to adipogenesis and function of adipocytes in fat of hospitalized dogs. Gonadal adipose tissues were collected from a total of 29 dogs, and the gene expression levels were examined by quantitative RT-PCR analysis. The multicollinearity analysis revealed that body condition score (BCS), which reflects adiposity, did not correlate with expression levels of any genes but correlated with age of dog. Bone morphogenetic protein (BMP) pathway stimulates not only commitment of mesenchymal stem cells to white adipocyte-lineage cells but also brown/beige adipogenesis. Some relationships between expression levels of BMP receptors were significant; especially, expression levels of activin receptor-like kinase (Alk) 3 (a BMP type I receptor) positively related to those of Alk2 (another BMP type I receptor), activin receptor type II (ActRII) A (a type II receptor to transmit BMP signal), ActRIIB (another type II receptor to transmit BMP signal) and BMP receptor type 2 (Bmpr2). PR domain containing 16 (Prdm16) expression levels strongly correlated with expression levels of ActRIIB. Although PRDM16 is known to stimulate brown/beige adipogenesis, expression levels of Ucp1 did not correlate with those of Prdm16. On the other hand, expression levels of Ucp1 correlated with those of Alk6. The present study suggests close relationships among adipose expressions of BMP signal components, and the relationships of expression levels of BMP receptor and those of Prdm16 or Ucp1 in dogs. Further studies using more dogs with various BCS potentially lead to identification of adipose factors to relate with adiposity in dogs.