Development and evaluation of a milk protein transcript depletion method for differential transcriptome analysis in mammary gland tissue

Allele-biased expression of the bovine APOB gene associated with the cholesterol deficiency defect suggests cis-regulatory enhancer effects of the LTR retrotransposon insertion

The insertion of an endogenous retroviral long terminal repeat (LTR) sequence into the bovine apolipoprotein B (APOB) gene is causal to the inherited genetic defect cholesterol deficiency (CD) observed in neonatal and young calves. Affected calves suffer from developmental abnormalities, symptoms of incurable diarrhoea and often die within weeks to a few months after birth. Neither the detailed effects of the LTR insertion on APOB expression profile nor the specific mode of inheritance nor detailed phenotypic consequences of the mutation are undisputed. In our study, we analysed German Holstein dairy heifers at the peak of hepatic metabolic load and exposed to an additional pathogen challenge for clinical, metabolic and hepatic transcriptome differences between wild type (CDF) and heterozygote carriers of the mutation (CDC). Our data revealed that a divergent allele-biased expression pattern of the APOB gene in heterozygous CDC animals leads to a tenfold higher expression of exons upstream and a decreased expression of exons downstream of the LTR insertion compared to expression levels of CDF animals. This expression pattern could be a result of enhancer activity induced by the LTR insertion, in addition to a previously reported artificial polyadenylation signal. Thus, our data support a regulatory potential of mobile element insertions. With regard to the phenotype generated by the LTR insertion, heterozygote CDC carriers display significantly differential hepatic expression of genes involved in cholesterol biosynthesis and lipid metabolism. Phenotypically, CDC carriers show a significantly affected lipomobilization compared to wild type animals. These results reject a completely recessive mode of inheritance for the CD defect, which should be considered for selection decisions in the affected population. Exemplarily, our results illustrate the regulatory impact of mobile element insertions not only on specific host target gene expression but also on global transcriptome profiles with subsequent biological, functional and phenotypic consequences in a natural in-vivo model of a non-model mammalian organism.

Investigation of the pathophysiology of bacterial mastitis using precision-cut bovine udder slices

Mastitis in cattle is a major health problem as well as incurring high costs for the dairy industry. To assess the suitability of precision-cut bovine udder slices (PCBUS) for bovine mastitis studies, we infected PCBUS with 2 different Staphylococcus aureus strains. Accordingly, we investigated both the tissue response to infection based on immune mediators at the mRNA and protein levels and the invasion of bacteria within the tissue. The studied proteins represent immune mediators of early inflammation [IL-1β, tumor necrosis factor-α (TNF-α), prostaglandin E₂ (PGE₂)] and showed a time-dependent increase in concentration. Infection of PCBUS with S. aureus resulted in increased expression of proinflammatory cytokines and chemokines such as TNF-α, C-C motif chemokine ligand 20 (CCL20), IL-1β, IL-6, and IL-10, but not C-X-C motif chemokine ligand 8 (CXCL8), lingual antimicrobial peptide (LAP), or S100 calcium binding protein A9 (S100A9) at the mRNA level. To compare the data acquired with this model, we carried out investigations on primary bovine mammary epithelial cells. Our results showed that the immune responses of both models-PCBUS and primary bovine mammary epithelial cells-were similar. In addition, investigations using PCBUS enabled us to demonstrate adherence of bacteria in the physiological cell network. These findings support the use of PCBUS in studies designed to further understand the complex pathophysiological processes of infection and inflammation in bovine mastitis and to investigate alternative therapies for mastitis.

Single-cell RNA sequencing of freshly isolated bovine milk cells and cultured primary mammary epithelial cells

Bovine mammary function at molecular level is often studied using mammary tissue or primary bovine mammary epithelial cells (pbMECs). However, bulk tissue and primary cells are heterogeneous with respect to cell populations, adding further transcriptional variation in addition to genetic background. Thus, understanding of the variation in gene expression profiles of cell populations and their effect on function are limited. To investigate the mononuclear cell composition in bovine milk, we analyzed a single-cell suspension from a milk sample. Additionally, we harvested cultured pbMECs to characterize gene expression in a homogeneous cell population. Using the Drop-seq technology, we generated single-cell RNA datasets of somatic milk cells and pbMECs. The final datasets after quality control filtering contained 7,119 and 10,549 cells, respectively. The pbMECs formed 14 indefinite clusters displaying intrapopulation heterogeneity, whereas the milk cells formed 14 more distinct clusters. Our datasets constitute a molecular cell atlas that provides a basis for future studies of milk cell composition and gene expression, and could serve as reference datasets for milk cell analysis.