Analysis of transcription regulator gene networks in peripartal bovine liver during summer and spring seasons
Gene network analysis was used on hepatic transcriptome data from cows calving during spring (SP) or summer (SU) to uncover transcription regulators (TR) and their target genes. Liver tissue was harvested from multiparous Holstein cows at -30, 3, and 35 d relative to parturition during SP (March-April, n = 6) and SU (June-July, n = 6). Mean temperature-humidity indeces for SP (day/night, below 72) and SU (day, 79.5 ± 2.9; night, 70.1 ± 4.7) were recorded. Transcriptomics was conducted using the 45K-Agilent bovine microarray. Statistical analysis with FDR ≤ 0.10 resulted in 618, 1,030 and 894 differentially expressed genes during SU vs. SP at -30, 3 and 35 d, respectively. Ingenuity pathway analysis (IPA) was used for gene network reconstructions. Among molecular and cellular functions, the IPA analysis identified cell death and survival and cellular growth and development as the most-enriched functions. Carbohydrate metabolism was the most enriched at -30 and 3 d, while nucleic acid metabolism and cellular development were the most enriched at 3 and 35 d. A total of 50, 78 and 74 TR were identified at -30, 3 and 35 d. The IPA analysis uncovered HNF4A, MYC, and NCOA1 (-30, 3 and 35 d), STAT3, and RELA (-30 and 35 d), BCL6 (3 and 35 d), KAT2B (-30 d), and GATA2 (3 d) as key TR. Comparing SU vs. SP at -30d uncovered HNF4A and MYC (both triggered by RELA) as key TR. Both are linked with several downstream up-regulated target genes involved in oxidation of xenobiotic compounds (CYP3A4), tryptophan catabolism (ACMSD1), arginine catabolism (ARG1), apoptosis regulation, and ER Calcium homeostasis (CFLAR, TMBIM6). In contrast, among the down-regulated targets there were several involved in cellular proliferation, anti-apoptotic activities, immune related disorders (CDKN1, LGALS1, TSPO), and liver disease (SERPINA1, FTH1). At 3 d, both HNF4A and MYC were down-regulated. Up-regulation of BCL6 was directly linked with the IL-6-dependent immune-response and cell growth. In contrast, BCL6 was associated with down-regulation of IL7R, IL13R1 and CXCL10-dependent immune responses. At 35 d, the up-regulation of RELA was associated with target genes involved in activation of anti-inflammatory responses (CCL3, B2M), extracellular matrix breakdown (MMP1), regulation of cell cycle (MYC, PTEN, CASP8) and gluconeogenesis (PCK1). These results suggests that the molecular phenotype of the liver differs when calving during the summer compared with spring.
Keywords: Temperature-humidity index, Transcription regulator network analysis, Transition cows