Adipogenic and energy metabolism gene networks in longissimus lumborum during rapid post-weaning growth in Angus and Angus × Simmental cattle fed high-starch or low-starch diets

<p>Abstract</p> <p>Background</p> <p>Transcriptional networks coordinate adipocyte differentiation and energy metabolism in rodents. The level of fiber and starch in diets with adequate energy content fed to young cattle has the potential to alter intramuscular adipose tissue development in skeletal muscle. Post-weaning alterations in gene expression networks driving adipogenesis, lipid filling, and intracellular energy metabolism provide a means to evaluate long-term effects of nutrition on longissimus muscle development across cattle types.</p> <p>Results</p> <p><it>Longissimus lumborum </it>(LL) from Angus (n = 6) and Angus × Simmental (A × S; n = 6) steer calves (155 ± 10 days age) fed isonitrogenous high-starch (HiS; 1.43 Mcal/kg diet dry matter; n = 6) or low-starch (LoS; 1.19 Mcal/kg diet dry matter; n = 6) diets was biopsied at 0, 56, and 112 days of feeding for transcript profiling of 31 genes associated with aspects of adipogenesis and energy metabolism. Intake of dietary energy (9.44 ± 0.57 Mcal/d) across groups during the study did not differ but feed efficiency (weight gain/feed intake) during the first 56 days was greater for steers fed HiS. Expression of <it>PPARG </it>increased ca. 2-fold by day 56 primarily due to HiS in A × S steers. Several potential <it>PPARG</it>-target genes (e.g., <it>ACACA</it>, <it>FASN</it>, <it>FABP4</it>, <it>SCD</it>) increased 2.5-to-25-fold by day 56 across all groups, with responses (e.g., <it>FASN</it>, <it>FABP4</it>) being less pronounced in A × S steers fed LoS. This latter group of steers had markedly greater blood plasma glucose (0.99 vs. 0.79 g/L) and insulin (2.95 vs. 1.17 μg/L) by day 112, all of which were suggestive of insulin resistance. Interactions were observed for <it>FABP4</it>, <it>FASN</it>, <it>GPAM</it>, <it>SCD</it>, and <it>DGAT2</it>, such that feeding A × S steers high-starch and Angus steers low-starch resulted in greater fold-changes by day 56 or 112 (<it>GPAM</it>). Marked up-regulation of <it>INSIG1 </it>(4-to-8-fold) occurred throughout the study across all groups. <it>SREBF1 </it>expression, however, was only greater on day 112 namely due to LoS in A × S steers. The lipogenic transcription factor <it>THRSP </it>was 6-to-60-fold greater by day 56 primarily due to HiS in A × S steers, constituting the greatest response among all genes.</p> <p>Conclusion</p> <p>Results involving gene markers of mature adipocytes (e.g., <it>PPARG</it>, <it>THRSP</it>, <it>SCD</it>) provided evidence of intramuscular adipose tissue differentiation during the early portion of the growing phase. The resulting gene networks underscored a central role for <it>PPARG </it>in controlling transcription of genes which are known to co-ordinately regulate adipocyte differentiation and lipid filling in non-ruminants. Unlike rodents, <it>INSIG1 </it>appears to play an important role in cattle muscle adipogenesis. We propose that a network of transcription regulators and nuclear receptors including <it>PPARG</it>-target genes,<it> INSIG1</it>, and <it>THRSP</it>, coordinate activation of adipocyte differentiation and lipid filling at an early age.</p

Internal controls for quantitative polymerase chain reaction of swine mammary glands during pregnancy and lactation.

High-throughput microarray analysis is an efficient means of obtaining a genome-wide view of transcript profiles across physiological states. However, quantitative PCR (qPCR) remains the chosen method for high-precision mRNA abundance analysis. Essential for reliability of qPCR data is normalization using appropriate internal control genes (ICG), which is now, more than ever before, a fundamental step for accurate gene expression profiling. We mined mammary tissue microarray data on >13,000 genes at -34, -14, 0, 7, 14, 21, and 28 d relative to parturition in 27 crossbred primiparous gilts to identify suitable ICG. Initial analysis revealed TBK1, PCSK2, PTBP1, API5, VAPB, QTRT1, TRIM41, TMEM24, PPP2R5B, and AP1S1 as the most stable genes (sample/reference = 1 +/- 0.2). We also included 9 genes previously identified as ICG in bovine mammary tissue. Gene network analysis of the 19 genes identified AP1S1, API5, MTG1, VAPB, TRIM41, MRPL39, and RPS15A as having no known co-regulation. In addition, UXT and ACTB were added to this list, and mRNA abundance of these 9 genes was measured by qPCR. Expression of all 9 of these genes was decreased markedly during lactation. In a previous study with bovine mammary tissue, mRNA of stably expressed genes decreased during lactation due to a dilution effect brought about by large increases in expression of highly abundant genes. To verify this effect, highly abundant mammary genes such as CSN1S2, SCD, FABP3, and LTF were evaluated by qPCR. The tested ICG had a negative correlation with these genes, demonstrating a dilution effect in the porcine mammary tissue. Gene stability analysis identified API5, VABP, and MRPL39 as the most stable ICG in porcine mammary tissue and indicated that the use of those 3 genes was most appropriate for calculating a normalization factor. Overall, results underscore the importance of proper validation of internal controls for qPCR and highlight the limitations of using absence of time effects as the criteria for selection of appropriate ICG. Further, we showed that use of the same ICG from one organism might not be suitable for qPCR normalization in other species

Old and New Stories: Revelations from Functional Analysis of the Bovine Mammary Transcriptome during the Lactation Cycle

The cow mammary transcriptome was explored at −30, −15, 1, 15, 30, 60, 120, 240, and 300 d relative to parturition. A total of 6,382 differentially expressed genes (DEG) at a false discovery rate ≤0.001 were found throughout lactation. The greatest number of DEG (>3,500 DEG) was observed at 60 and 120 d vs. −30 d with the largest change between consecutive time points observed at −15 vs. 1 d and 120 vs. 240 d. Functional analysis of microarray data was performed using the Dynamic Impact Approach (DIA). The DIA analysis of KEGG pathways uncovered as the most impacted and induced ‘Galactose metabolism’, ‘Glycosylphosphatidylinositol (GPI)-anchor biosynthesis’, and ‘PPAR signaling’; whereas, ‘Antigen processing and presentation’ was among the most inhibited. The integrated interpretation of the results suggested an overall increase in metabolism during lactation, particularly synthesis of carbohydrates and lipid. A marked degree of utilization of amino acids as energy source, an increase of protein export, and a decrease of the protein synthesis machinery as well cell cycle also were suggested by the DIA analysis. The DIA analysis of Gene Ontology and other databases uncovered an induction of Golgi apparatus and angiogenesis, and the inhibition of both immune cell activity/migration and chromosome modifications during lactation. All of the highly-impacted and activated functions during lactation were evidently activated at the onset of lactation and inhibited when milk production declined. The overall analysis indicated that the bovine mammary gland relies heavily on a coordinated transcriptional regulation to begin and end lactation. The functional analysis using DIA underscored the importance of genes associated with lactose synthesis, lipid metabolism, protein synthesis, Golgi, transport, cell cycle/death, epigenetic regulation, angiogenesis, and immune function during lactation

Gene network and pathway analysis of bovine mammary tissue challenged with Streptococcus uberis reveals induction of cell proliferation and inhibition of PPARγ signaling as potential mechanism for the negative relationships between immune response and lipid metabolism

<p>Abstract</p> <p>Background</p> <p>Information generated via microarrays might uncover interactions between the mammary gland and <it>Streptococcus uberis </it>(<b><it>S. uberis</it></b>) that could help identify control measures for the prevention and spread of <it>S. uberis </it>mastitis, as well as improve overall animal health and welfare, and decrease economic losses to dairy farmers. The main objective of this study was to determine the most affected gene networks and pathways in mammary tissue in response to an intramammary infection (<b>IMI</b>) with <it>S. uberis </it>and relate these with other physiological measurements associated with immune and/or metabolic responses to mastitis challenge with <it>S. uberis </it>O140J.</p> <p>Results</p> <p><it>Streptococcus uberis </it>IMI resulted in 2,102 (1,939 annotated) differentially expressed genes (<b>DEG</b>). Within this set of DEG, we uncovered 20 significantly enriched canonical pathways (with 20 to 61 genes each), the majority of which were signaling pathways. Among the most inhibited were <it>LXR/RXR Signaling </it>and <it>PPARα/RXRα Signaling</it>. Pathways activated by IMI were <it>IL-10 Signaling </it>and <it>IL-6 Signaling </it>which likely reflected counter mechanisms of mammary tissue to respond to infection. Of the 2,102 DEG, 1,082 were up-regulated during IMI and were primarily involved with the immune response, e.g., <it>IL6</it>, <it>TNF</it>, <it>IL8, IL10, SELL, LYZ</it>, and <it>SAA3</it>. Genes down-regulated (1,020) included those associated with milk fat synthesis, e.g., <it>LPIN1, LPL, CD36</it>, and <it>BTN1A1</it>. Network analysis of DEG indicated that <it>TNF </it>had positive relationships with genes involved with immune system function (e.g., <it>CD14, IL8, IL1B</it>, and <it>TLR2</it>) and negative relationships with genes involved with lipid metabolism (e.g., <it>GPAM</it>, <it>SCD</it>, <it>FABP4</it>, <it>CD36</it>, and <it>LPL</it>) and antioxidant activity (<it>SOD1</it>).</p> <p>Conclusion</p> <p>Results provided novel information into the early signaling and metabolic pathways in mammary tissue that are associated with the innate immune response to <it>S. uberis </it>infection. Our study indicated that IMI challenge with <it>S. uberis </it>(strain O140J) elicited a strong transcriptomic response, leading to potent activation of pro-inflammatory pathways that were associated with a marked inhibition of lipid synthesis, stress-activated kinase signaling cascades, and PPAR signaling (most likely PPARγ). This latter effect may provide a mechanistic explanation for the inverse relationship between immune response and milk fat synthesis.</p

Blood immunometabolic indices and polymorphonuclear neutrophil function in peripartum dairy cows are altered by level of dietary energy prepartum

Cows experience some degree of negative energy balance and immunosuppression around parturition, making them vulnerable to metabolic and infectious diseases. The effect of prepartum feeding of diets to meet (control, 1.34 Mcal/kg of dry matter) or exceed (overfed, 1.62 Mcal/kg of dry matter) dietary energy requirements was evaluated during the entire dry period (∼45 d) on blood polymorphonuclear neutrophil function, blood metabolic and inflammatory indices, and milk production in Holstein cows. By design, dry matter intake in the overfed group (n=9) exceeded energy requirements during the prepartum period (-4 to -1 wk relative to parturition), resulting in greater energy balance when compared with the control group (n=10). Overfed cows were in more negative energy balance during wk 1 after calving than controls. No differences were observed in dry matter intake, milk yield, and milk composition between diets. Although nonesterified fatty acid concentration pre- (0.138 mEq/L) and postpartum (0.421 mEq/L) was not different between diets, blood insulin concentration was greater in overfed cows prepartum (16.7 μIU/mL) compared with controls pre- and postpartum (∼3.25 μIU/mL). Among metabolic indicators, concentrations of urea (4.63 vs. 6.38 mmol/L), creatinine (100 vs. 118 μmol/L), and triacylglycerol (4.0 vs. 8.57 mg/dL) in overfed cows were lower prepartum than controls. Glucose was greater pre- (4.24 vs. 4.00 mmol/L) and postpartum (3.49 vs. 3.30 mmol/L) compared with control cows. Among liver function indicators, the concentration of bilirubin increased by 2 to 6 fold postpartum in control and overfed cows. Phagocytosis capacity of polymorphonuclear neutrophils was lower prepartum in overfed cows (32.7% vs. 46.5%); phagocytosis in the control group remained constant postpartum (50%) but it increased at d 7 in the overfed group to levels similar to controls (48.4%). Regardless of prepartum diet, parturition was characterized by an increase in nonesterified fatty acid and liver triacylglycerol, as well as blood indices of inflammation (ceruloplasmin and haptoglobin), oxidative stress (reactive oxygen metabolites), and liver injury (glutamic oxaloacetic transaminase). Concentrations of the antioxidant and anti-inflammatory compounds vitamin A, vitamin E, and β-carotene decreased after calving. For vitamin A, the decrease was observed in overfed cows (47.3 vs. 27.5 μg/100 mL). Overall, overfeeding energy and higher energy status prepartum led to the surge of insulin and had a transient effect on metabolism postpartum

Functional and gene network analyses of transcriptional signatures characterizing pre-weaned bovine mammary parenchyma or fat pad uncovered novel inter-tissue signaling networks during development

<p>Abstract</p> <p>Background</p> <p>The neonatal bovine mammary fat pad (<b>MFP</b>) surrounding the mammary parenchyma (<b>PAR</b>) is thought to exert proliferative effects on the PAR through secretion of local modulators of growth induced by systemic hormones. We used bioinformatics to characterize transcriptomics differences between PAR and MFP from ~65 d old Holstein heifers. Data were mined to uncover potential crosstalk through the analyses of signaling molecules preferentially expressed in one tissue relative to the other.</p> <p>Results</p> <p>Over 9,000 differentially expressed genes (<b>DEG</b>; False discovery rate ≤ 0.05) were found of which 1,478 had a ≥1.5-fold difference between PAR and MFP. Within the DEG highly-expressed in PAR vs. MFP (n = 736) we noted significant enrichment of functions related to cell cycle, structural organization, signaling, and DNA/RNA metabolism. Only actin cytoskeletal signaling was significant among canonical pathways. DEG more highly-expressed in MFP vs. PAR (n = 742) belong to lipid metabolism, signaling, cell movement, and immune-related functions. Canonical pathways associated with metabolism and signaling, particularly immune- and metabolism-related were significantly-enriched. Network analysis uncovered a central role of <it>MYC</it>, <it>TP53</it>, and <it>CTNNB1 </it>in controlling expression of DEG highly-expressed in PAR vs. MFP. Similar analysis suggested a central role for <it>PPARG</it>, <it>KLF2</it>, <it>EGR2</it>, and <it>EPAS1 </it>in regulating expression of more highly-expressed DEG in MFP vs. PAR. Gene network analyses revealed putative inter-tissue crosstalk between cytokines and growth factors preferentially expressed in one tissue (e.g., <it>ANGPTL1</it>, <it>SPP1</it>, <it>IL1B </it>in PAR vs. MFP; <it>ADIPOQ</it>, <it>IL13</it>, <it>FGF2</it>, <it>LEP </it>in MFP vs. PAR) with DEG preferentially expressed in the other tissue, particularly transcription factors or pathways (e.g., <it>MYC</it>, <it>TP53</it>, and actin cytoskeletal signaling in PAR vs. MFP; <it>PPARG </it>and LXR/RXR Signaling in MFP vs. PAR).</p> <p>Conclusions</p> <p>Functional analyses underscored a reciprocal influence in determining the biological features of MFP and PAR during neonatal development. This was exemplified by the potential effect that the signaling molecules (cytokines, growth factors) released preferentially (i.e., more highly-expressed) by PAR or MFP could have on molecular functions or signaling pathways enriched in the MFP or PAR. These bidirectional interactions might be required to coordinate mammary tissue development under normal circumstances or in response to nutrition.</p

RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high- and low-residual feed intake in Nordic dairy cattle

BACKGROUND: The selective breeding of cattle with high-feed efficiencies (FE) is an important goal of beef and dairy cattle producers. Global gene expression patterns in relevant tissues can be used to study the functions of genes that are potentially involved in regulating FE. In the present study, high-throughput RNA sequencing data of liver biopsies from 19 dairy cows were used to identify differentially expressed genes (DEGs) between high- and low-FE groups of cows (based on Residual Feed Intake or RFI). Subsequently, a profile of the pathways connecting the DEGs to FE was generated, and a list of candidate genes and biomarkers was derived for their potential inclusion in breeding programmes to improve FE. RESULTS: The bovine RNA-Seq gene expression data from the liver was analysed to identify DEGs and, subsequently, identify the molecular mechanisms, pathways and possible candidate biomarkers of feed efficiency. On average, 57 million reads (short reads or short mRNA sequences < ~200 bases) were sequenced, 52 million reads were mapped, and 24,616 known transcripts were quantified according to the bovine reference genome. A comparison of the high- and low-RFI groups revealed 70 and 19 significantly DEGs in Holstein and Jersey cows, respectively. The interaction analysis (high vs. low RFI x control vs. high concentrate diet) showed no interaction effects in the Holstein cows, while two genes showed interaction effects in the Jersey cows. The analyses showed that DEGs act through certain pathways to affect or regulate FE, including steroid hormone biosynthesis, retinol metabolism, starch and sucrose metabolism, ether lipid metabolism, arachidonic acid metabolism and drug metabolism cytochrome P450. CONCLUSION: We used RNA-Seq-based liver transcriptomic profiling of high- and low-RFI dairy cows in two breeds and identified significantly DEGs, their molecular mechanisms, their interactions with other genes and functional enrichments of different molecular pathways. The DEGs that were identified were the CYP’s and GIMAP genes for the Holstein and Jersey cows, respectively, which are related to the primary immunodeficiency pathway and play a major role in feed utilization and the metabolism of lipids, sugars and proteins. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3622-9) contains supplementary material, which is available to authorized users