Abstract
Using published dairy cattle liver transcriptomics dataset along with novel blood biomarkers of liver function, metabolism, and inflammation we have attempted an integrative systems biology approach applying the classical functional enrichment analysis using DAVID, a newly-developed Dynamic Impact Approach (DIA), and an upstream gene network analysis using Ingenuity Pathway Analysis (IPA). Transcriptome data was generated from experiments evaluating the impact of prepartal plane of energy intake [overfed (OF) or restricted (RE)] on liver of dairy cows during the peripartal period. Blood biomarkers uncovered that RE vs. OF led to greater prepartal liver distress accompanied by a low-grade inflammation and larger proteolysis (i.e., higher haptoglobin, bilirubin, and creatinine). Post-partum the greater bilirubinaemia and lipid accumulation in OF vs. RE indicated a large degree of liver distress. The re-analysis of microarray data revealed that expression of >4,000 genes was affected by diet × time. The bioinformatics analysis indicated that RE vs. OF cows had a liver with a greater lipid and amino acid catabolic capacity both pre- and post-partum while OF vs. RE cows had a greater activation of pathways/functions related to triglyceride synthesis. Furthermore, RE vs. OF cows had a larger (or higher capacity to cope with) ER stress likely associated with greater protein synthesis/processing, and a higher activation of inflammatory-related functions. Liver in OF vs. RE cows had a larger cell proliferation and cell-to-cell communication likely as a response to the greater lipid accumulation. Analysis of upstream regulators indicated a pivotal role of several lipid-related transcription factors (e.g., PPARs, SREBPs, and NFE2L2) in priming the liver of RE cows to better face the early postpartal metabolic and inflammatory challenges. An all-encompassing dynamic model was proposed based on the findings.
Highlights
The liver performs essential functions in mammals
We reported previously that prepartal high dietary energy (OF) vs. feed restriction (RE) markedly increased prepartal insulin concentration and early postpartum concentration of NEFA, BHBA, total protein, and liver TAG
Biological interpretation of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in combination with Gene Ontology and enrichment analyses Here we provide an integral view of the pathways combining the Dynamic Impact Approach (DIA) results (File S2) with the visual results of several pathways obtained via KegArray (File S3) plus DIA results of Gene Ontology (GO) biological process (Files S2 and S4) and enrichment analysis performed using DAVID (Figure 4 and File S5 for details)
Summary
The liver performs essential functions in mammals These include, but are not limited to, gluconeogenesis and glycogen synthesis, synthesis of several plasma proteins encompassing clotting factors and acute phase proteins (APP) (e.g., haptoglobin, albumin, and fibrinogen), metabolism of amino acids and lipids, and detoxification including ammonia removal [1,2]. During the period around parturition in dairy cattle, known as the peripartal or ‘‘transition period’’ [2], the importance of the liver becomes even more critical due to the greater metabolic demands imposed by the onset of lactation, the need to increase gluconeogenesis, fatty acid metabolism, and to control the inflammatory response [3,4]. Transcriptome profiling studies of peripartal cattle demonstrated molecular adaptations in this organ some of which could alter its function, e.g. immune response and lipid metabolism [8,9,10]. The aggregation of the transcriptomics dataset from cows fed recommended [9] or different levels of energy prepartum [10] revealed an extremely large effect of OF or restricting energy (RE) prepartum on the transcriptome adaptations during the transition period with a very modest effect observed when cows were fed recommended levels of energy [11]
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