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

Abstract

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.

Milk Protein Synthesis in the Lactating Mammary Gland: Insights from Transcriptomics Analyses

“…The above observations support the importance of transcriptional regulation of the milk proteins, as also previously suggested for dairy cows [34]. However, some of the data (e.g., patterns of expression and milk content of LTF in sows) might indicate that the abundance of some of the most enriched proteins in milk is regulated post-translationally, as previously shown [88].…”

“…The AA in mammary gland in dairy cows are not solely used for protein synthesis, but also for production of energy through the Krebs cycle [12,33]. Our recent transcriptomics studies in dairy cattle from pregnancy to lactation support that conclusion [34].…”

“…In addition, we observed a large increase in expression during lactation of several AA transporters, particularly the one transporting branched-chain amino acids and the one related to mTOR activity (e.g., see leucine activity on mTOR above), as well as the three glucose transporters known to be important in bovine mammary [4]. The large increase in expression of those transporters strongly supports the known increase in mammary uptake of glucose and AA during lactation; however, this also suggests that the energy level inside the mammary gland increases, thereby preventing the indirect mTOR inhibition by AMPK (mostly through the use of AA, see [34]). …”

“…General references [67,68]. Specific references for milk composition are: bovine [4,67,69], mouse and rat [70][71][72][73][74], human [75], pig [55], sheep and goat [76], and Kangaroo [77][78][79] The application of functional genomics and bioinformatics allows for a thorough exploration of the biological complexity of organisms' tissues [34]. Together, these approaches form part of the systems biology framework, i.e., a way to systematically study the complex interactions in biological systems using a method of integration instead of reduction.…”

“…The plethora of phenomena happening in this tissue during all the developmental phases make it suitable for study by 'omics' technologies; particularly useful has been application of microarray technology to study gene and miRNA expression. Several studies have been published about the use of microarray technologies to investigate transcriptomics adaptation of mammary gland during development, lactation, and involution (some references among others [34,[172][173][174][175][176]). Also the use of microarrays to study the miRNA in mammary gland development has seeing an increase in popularity [177][178][179].…”