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

Abstract

BackgroundThe neonatal bovine mammary fat pad (MFP) surrounding the mammary parenchyma (PAR) 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.ResultsOver 9,000 differentially expressed genes (DEG; 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 MYC, TP53, and CTNNB1 in controlling expression of DEG highly-expressed in PAR vs. MFP. Similar analysis suggested a central role for PPARG, KLF2, EGR2, and EPAS1 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., ANGPTL1, SPP1, IL1B in PAR vs. MFP; ADIPOQ, IL13, FGF2, LEP in MFP vs. PAR) with DEG preferentially expressed in the other tissue, particularly transcription factors or pathways (e.g., MYC, TP53, and actin cytoskeletal signaling in PAR vs. MFP; PPARG and LXR/RXR Signaling in MFP vs. PAR).ConclusionsFunctional 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.

Differences in Gene Expression and Cytokine Release Profiles Highlight the Heterogeneity of Distinct Subsets of Adipose Tissue-Derived Stem Cells in the Subcutaneous and Visceral Adipose Tissue in Humans

“…Briefly, the dataset containing gene identifiers and corresponding fold changes was uploaded into the web-delivered application, and each gene identifier was mapped to its corresponding gene object. The threshold for a significant association was determined by the p -value <0.01, becoming significant any score above 3 [24]; [25]. For all analyses, Fisher’s exact test was used to calculate a p -value and to determine a score for all networks that were ranked on the probability that a collection of genes equal to or greater than the number in a network could be achieved by chance alone.…”

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

“…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].…”

Expression of NGF, BDNF and their high-affinity receptors in ovine mammary glands during development and lactation

“…Interactions between parenchyma and mammary fat pad are also demonstrated in prepubertal ewes (Hovey et al 1998), suggesting the presence of epithelial paracrine factors that would exert a positive feedback on the surrounding stroma. Interestingly, in a paper of Piantoni et al (2010) the transcriptomic differences analysis on 65-day-old Holstein heifers showed a bidirectional regulation between mammary fat pad and parenchyma. Cytokines and growth factors preferentially released by parenchyma were related to cell cycle progression, while those released by fat pad were involved in lipid metabolism and molecular transport.…”

“…Cytokines and growth factors preferentially released by parenchyma were related to cell cycle progression, while those released by fat pad were involved in lipid metabolism and molecular transport. Moreover, the expression and secretion of leptin in mammary fat pad were thought to influence the expression of BDNF in the parenchyma (Piantoni et al 2010). Other transcriptome analyses were separately conducted on epithelial and intralobular stromal compartments of non-lactating dairy cows 3 weeks prepartum.…”